diff --git a/doc_build/_build/html/.buildinfo b/doc_build/_build/html/.buildinfo deleted file mode 100644 index 04795d10..00000000 --- a/doc_build/_build/html/.buildinfo +++ /dev/null @@ -1,4 +0,0 @@ -# Sphinx build info version 1 -# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: b81ec02fcdf8902e921a11938e202641 -tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/doc_build/_build/html/_sources/anaconda_install.rst.txt b/doc_build/_build/html/_sources/anaconda_install.rst.txt deleted file mode 100644 index 349ba274..00000000 --- a/doc_build/_build/html/_sources/anaconda_install.rst.txt +++ /dev/null @@ -1,47 +0,0 @@ -.. _anaconda_installation: - -Installing Miniconda (Mac, Linux) -================================= - -Anaconda is a very large install, containing not only Python, but also R, and a host of other things that are not necessary to run pyleoclim. -Users may find it preferable to install the more minimalist "miniconda" package. - -Step 1: Download the installation script for miniconda3 -"""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -MacOS ------ - -.. code-block:: bash - - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh - -Linux ------ -.. code-block:: bash - - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh - -Step 2: Install Miniconda3 -""""""""""""""""""""""""""" - -.. code-block:: bash - - chmod +x Miniconda3-latest-*.sh && ./Miniconda3-latest-Linux-x86_64.sh - -During the installation, a path `` needs to be specified as the base location of the python environment. -After the installation is done, we need to add the two lines into your shell environment (e.g., `~/.bashrc` or `~/.zshrc`) as below to enable the `conda` package manager (remember to change `` with your real location): - -.. code-block:: bash - - export PATH="/bin:$PATH" - . /etc/profile.d/conda.sh - -Step 3: Test your Installation -""""""""""""""""""""""""""""""" - -.. code-block:: bash - - source ~/.bashrc # assume you are using Bash shell - which python # should return a path under - which conda # should return a path under diff --git a/doc_build/_build/html/_sources/citation.rst.txt b/doc_build/_build/html/_sources/citation.rst.txt deleted file mode 100644 index c4f75ad5..00000000 --- a/doc_build/_build/html/_sources/citation.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -.. _citing_pyleoclim: - -Citing Pyleoclim -================ - -If Pyleoclim played an important part in your research, please add us to your reference list by using one of the citations below. - -BibTeX entry -""""""""""""" - -For example (please check for version updates on Zenodo) - -@misc{Pyleoclim, - DOI= {10.5281/zenodo.1205661}, - url = {https://doi.org/10.5281/zenodo.1205661}, - year = {2021}, - type = {Computer Program} - title = {Pyleoclim: A Python package for the analysis of paleoclimate data}, - authors = {Deborah Khider and Feng Zhu and Julien Emile-Geay and Jun Hu and Alexander James and Pratheek Athreya and Myron Kwan and Daniel Garijo} -} - - -AGU style entry -""""""""""""""" - -Khider, D. et al (2021). Pyleoclim: A Python package for the analysis of paleoclimate data. Retrieved from https://doi.org/10.5281/zenodo.1205661 diff --git a/doc_build/_build/html/_sources/contribution_guide.rst.txt b/doc_build/_build/html/_sources/contribution_guide.rst.txt deleted file mode 100644 index 4345c639..00000000 --- a/doc_build/_build/html/_sources/contribution_guide.rst.txt +++ /dev/null @@ -1,303 +0,0 @@ -.. _contributing_to_pyleoclim: - -######################### -Contributing to Pyleoclim -######################### - - -GitHub, GitHub, GitHub -======================= -All contributions, bug reports, bug fixes, documentation improvements, enhancements, -and ideas are welcome, and take place through `GitHub `_ - -There are several levels of contributions to an open development software package like Pyleoclim, including: - -#. Reporting Bugs -#. Updating the documentation -#. Updating existing functionalities -#. Contributing new functionalities - -All of that takes place through GitHub `issues `_, but we recommend first reaching out to our community Slack to avoid effort duplication (to get added to our Slack workspace, please email `LinkedEarth `_. - -When you start working on an issue, it’s a good idea to assign the issue to yourself, again to limit duplication. If you can’t think of an issue of your own, we have you covered: check the list of unassigned issues and assign yourself one you like. -If for whatever reason you are not able to continue working with the issue, please try to unassign it, so other people know it’s available again. You can check the list of assigned issues, since people may not be working in them anymore. If you want to work on one that is assigned, feel free to kindly ask the current assignee (on GitHub and/or Slack) if you can take it (please allow at least a week of inactivity before considering work in the issue discontinued). - -Bug reports and enhancement requests -==================================== - -Bug reports are an important part of improving any software. Having a complete bug report will allow others to reproduce the bug and provide insight into fixing. See this `stackoverflow article` `_ and `this blogpost `_ for tips on writing a good bug report. -Trying the bug*producing code out on the master branch is often a worthwhile exercise to confirm the bug still exists. It is also worth searching existing bug reports and pull requests to see if the issue has already been reported and/or fixed. -Bug reports must: - -1. Include a minimal working example (a short, self*contained Python snippet reproducing the problem). You can format the code nicely by using GitHub Flavored Markdown:: - - import pyleoclim as pyleo - url = 'https://raw.githubusercontent.com/LinkedEarth/Pyleoclim_util/Development/example_data/lipds.json' - response = urlopen(url) - D = json.loads(response.read()) - d = pyleo.Lipd(lipd_dict=D) - ts = d.to_LipdSeries(number=6) - res=ts.mapNearRecord(d,mute=True) - -2. Include the full version string of pyleoclim, which you can obtain through:: - - pyleo.__version__ - -3. Explain why the current behavior is wrong/not desired and what you expect or would like to see instead. - - -Working with the Pyleoclim codebase -=================================== -Version control, Git, and GitHub -"""""""""""""""""""""""""""""""" - -To the neophyte, working with Git is one of the more daunting aspects of contributing to open source projects. -It can very quickly become overwhelming, but sticking to the guidelines below will help keep the process straightforward and mostly trouble free. As always, if you are having difficulties please feel free to ask for help. -The code is hosted on `GitHub `_. To contribute you will need to `sign up for a (free) GitHub account `_. `Git `_ is the industry standard for version control to allow many people to work together on the project, keep track of issues, manage the project, and much more. - -Some great resources for learning Git: - * the `GitHub help pages `_ - * the `NumPy documentation `_ - * Matthew Brett’s `Pydagogue `_ - -GitHub has `instructions `_ for installing git, setting up your SSH key, and configuring git. All these steps need to be completed before you can work seamlessly between your local repository and GitHub. - -Forking -""""""" -You will need your own fork to work on the code. Go to the Pyleoclim repository and hit the Fork button. You will then want to clone your fork (i.e. download all the code to your local machine so you can edit it locally). -At the command line, this would like something like:: - git clone https://github.com/your-user-name/Pyleoclim_util.git pyleoclim-yourname - cd pyleoclim-yourname - git remote add upstream https://github.com/LinkedEarth/Pyleoclim_util.git - -This creates the directory `pyleoclim-yourname` and connects your repository to the upstream (main project) Pyleoclim repository. However, most Git first-timers may find it easier to do so through the Github web interface or desktop app (where there is a proverbial “button for that”). - -Creating a development environment -"""""""""""""""""""""""""""""""""" -We recommend developing in the same conda environment in which you installed Pyleoclim. - -Creating a branch -""""""""""""""""" -You want your master branch to reflect only production*ready code, so create a feature branch for making your changes. For example:: - - git branch shiny-new-feature - git checkout shiny-new-feature - -The above can be simplified to:: - - git checkout -b shiny-new-feature - -This changes your working directory to the `shiny-new-feature` branch. Keep any changes in this branch specific to one bug or feature so it is clear what the branch brings to Pyleoclim. You can have many `shiny-new-features` and switch in between them using the `git checkout` command. -When creating this branch, make sure your master branch is up to date with the latest upstream master version. To update your local master branch, you can do:: - - git checkout master - git pull upstream master --ff-only - -When you want to update the feature branch with changes in master after you created the branch, check the section on updating a pull request. - -Pyleoclim Protocol -"""""""""""""""""" - -Contributing new functionalities -******************************** - - 1. Open an issue on GitHub (See above) - 2. Implement outside of Pyleoclim - Before incorporating any code into Pyleoclim, make sure you have a solution that works outside Pyleoclim. Demonstrate this in a notebook, which can be hosted on GitHub as well so it is easy for the maintainers to check out. The notebook should be organized as follows: - * dependencies (package names and versions), - * body of the function - * example usage - 3. Integrate the new functionality - Now you may implement the new functionality inside Pyleoclim. In so doing, make sure you: - * Re-use as many of Pyleoclim’s existing utilities as you can, introducing new package dependencies only as necessary. - * Create a docstring for your new function, describing arguments and returned variables, and showing an example of use. (Use an existing docstring for inspiration). - * If possible, also include a unit test for `continuous integration `_ (Pyleoclim uses `pytest` and `TravisCI`). Feel free to ask for help from the package developers. - 4. Expose the new functionality in the Pyleoclim API (`ui.py`) - - -Updating existing functionalities -********************************** - -1. Open an issue on GitHub (same advice as above) -2. Implement outside of Pyleoclim, including a benchmark of how the existing function performs vs the proposed upgrade (e.g. with `timeit`). Take into consideration memory requirements and describe on what architecture/OS you ran the test. -3. Integrate the new functionality within Pyleoclim (same advice as above) -4. Update the unit test(s) to make sure they still pass muster. Depending on the complexity of the feature, there may be more than one test to update. - -Testing -""""""" - -Testing is hugely important, as you don’t want your “upgrades” to break the whole package by introducing errors. Thankfully there is a proverbial app for that: *unit testing*. Write a test of your code using the naming rules: - -1. class: `Test{filename}{Class}{method}` with appropriate camel case convention -2. function: `test_{method}_t{test_id}` - -(see e.g. test_ui_Series.py for example) - -Your test should be as minimal as possible; it is aimed to see if the function your wrote/updated works as advertised given a reasonably comprehensive list of possible arguments. Pyleoclim’s tests rely on data already included in the example_data directory, and we strongly recommend that you do the same; only introduce a new dataset if the existing ones are insufficient to properly test your code. In general, the simpler the test, the better, as it will run in less time and won’t get the Travis gods angry with us. - -To run the test(s): - -0. Make sure the `pytest package `_ is installed on your system; run `pip install pytest` if not. -1. In your terminal, switch to the “tests” subdirectory of your Pyleoclim forked repository. If you wish to test a specific class/method inside a specified file, run -`pytest {file_path}::{TestClass}::{test_method}` - -2. To run *all* tests in the specified file, run `pytest {file_path}` - -3. To perform all tests in all testing files inside the specified directory, execute `pytest {directory_path}` - -The order above is somewhat loose, but goes from least complex (time*consuming) to more complex. - - -Stylistic considerations -""""""""""""""""""""""""" -Guido van Rossum’s great insight is that code is read far more often than it is written, so it is important for the code to be of a somewhat uniform style, so that people can read and understand it with relative ease. Pyleoclim strives to use fairly consistent notation, including: - - * capital letters for matrices, lowercase for vectors - * Independent variable is called ys, the dependent variable (the time axis) ts. - * Function names use CamelCase convention - -Contributing your changes to Pyleoclim -====================================== - -Committing your code -"""""""""""""""""""" -Once you’ve made changes, you can see them by typing:: - - git status - -If you created a new file, it is not being tracked by git. Add it by typing:: - - git add path/to/file-to-be-added.py - -Typing `git status` again should give something like:: - - On branch shiny-new-feature - modified: /relative/path/to/file-you-added.py - -Finally, commit your changes to your local repository with an explanatory message. The message need not be encyclopedic, but it should say what you did, what GitHub issue it refers to, and what part of the code it is expected to affect. -The preferred style is: - - * a subject line with < 80 chars. - * One blank line. - * Optionally, a commit message body. - -Now you can commit your changes in your local repository:: - - git commit -m 'type your message here' - -Pushing your changes -"""""""""""""""""""" - -When you want your changes to appear publicly on your GitHub page, push your forked feature branch’s commits:: - - git push origin shiny-new-feature - -Here `origin` is the default name given to your remote repository on GitHub. You can see the remote repositories:: - - git remote -v - -If you added the upstream repository as described above you will see something like:: - - origin git@github.com:yourname/Pyleoclim_util.git (fetch) - origin git@github.com:yourname/Pyleoclim_util.git (push) - upstream git://github.com/LinkedEarth/Pyleoclim_util.git (fetch) - upstream git://github.comLinkedEarth/Pyleoclim_util.git (push) - -Now your code is on GitHub, but it is not yet a part of the Pyleoclim project. For that to happen, a pull request needs to be submitted on GitHub. - -Filing a Pull Request -""""""""""""""""""""" -When you’re ready to ask for a code review, file a pull request. But before you do, please double*check that you have followed all the guidelines outlined in this document regarding code style, tests, performance tests, and documentation. You should also double check your branch changes against the branch it was based on: - - * Navigate to your repository on GitHub - * Click on Branches - * Click on the Compare button for your feature branch - * Select the base and compare branches, if necessary. This will be *Development* and *shiny-new-feature*, respectively. - -If everything looks good, you are ready to make a pull request. A pull request is how code from a local repository becomes available to the GitHub community and can be reviewed by a project’s owners/developers and eventually merged into the master version. This pull request and its associated changes will eventually be committed to the master branch and available in the next release. To submit a pull request: - - * Navigate to your repository on GitHub - * Click on the Pull Request button - * You can then click on Commits and Files Changed to make sure everything looks okay one last time - * Write a description of your changes in the Preview Discussion tab - * Click Send Pull Request. - -This request then goes to the repository maintainers, and they will review the code. - -Updating your pull request -"""""""""""""""""""""""""" - -Based on the review you get on your pull request, you will probably need to make some changes to the code. In that case, you can make them in your branch, add a new commit to that branch, push it to GitHub, and the pull request will be automatically updated. Pushing them to GitHub again is done by: -git push origin shiny-new-feature -This will automatically update your pull request with the latest code and restart the Continuous Integration tests (which is why it is important to provide a test for your code). -Another reason you might need to update your pull request is to solve conflicts with changes that have been merged into the master branch since you opened your pull request. -To do this, you need to `merge upstream master` in your branch:: - - git checkout shiny-new-feature - git fetch upstream - git merge upstream/master - -If there are no conflicts (or they could be fixed automatically), a file with a default commit message will open, and you can simply save and quit this file. -If there are merge conflicts, you need to solve those conflicts. See `this example `_ for an explanation on how to do this. Once the conflicts are merged and the files where the conflicts were solved are added, you can run git commit to save those fixes. -If you have uncommitted changes at the moment you want to update the branch with master, you will need to stash them prior to updating (see the stash docs). This will effectively store your changes and they can be reapplied after updating. -After the feature branch has been updated locally, you can now update your pull request by pushing to the branch on GitHub:: - - git push origin shiny-new-feature - -Delete your merged branch (optional) -"""""""""""""""""""""""""""""""""""" - -Once your feature branch is accepted into upstream, you’ll probably want to get rid of the branch. First, merge upstream master into your branch so git knows it is safe to delete your branch:: - - git fetch upstream - git checkout master - git merge upstream/master - -Then you can do:: - - git branch -d shiny-new-feature - -Make sure you use a lowercase `-d`, or else git won’t warn you if your feature branch has not actually been merged. -The branch will still exist on GitHub, so to delete it there do:: - - git push origin --delete shiny-new-feature - -Tips for a successful pull request -"""""""""""""""""""""""""""""""""" -If you have made it to the “Review your code” phase, one of the core contributors will take a look. Please note however that response time will be variable (e.g. don’t try the week before AGU). -To improve the chances of your pull request being reviewed, you should: - - * Reference an open issue for non*trivial changes to clarify the PR’s purpose - * Ensure you have appropriate tests. These should be the first part of any PR - * Keep your pull requests as simple as possible. Larger PRs take longer to review - * If you need to add on to what you submitted, keep updating your original pull request, either by request or every few days - -Documentation -============= - -About the Pyleoclim documentation -""""""""""""""""""""""""""""""""" -Pyleoclim's documentation is built automatically from the function and class docstrings, via `Read The Docs `_. It is therefore especially important for your code to include a docstring, and to modify the docstrings of the functions/classes you modified to make sure the documentation is current. - -Updating a Pyleoclim docstring -"""""""""""""""""""""""""""""" -You may use existing docstrings as examples. A good docstring explains: - - * what the function/class is about - * what it does, with what properties/inputs/outputs) - * how to use it, via a minimal working example. - -For the latter, make sure the example is prefaced by:: - - :okwarning: - :okexcept: - -and properly indented. - -How to build the Pyleoclim documentation -"""""""""""""""""""""""""""""""""""""""" - -Navigate to the doc_build folder and type `make html`. This may require installing other packages (sphinx, nbsphinx, etc). - - -You are done! Thanks for playing. diff --git a/doc_build/_build/html/_sources/core/ui.rst.txt b/doc_build/_build/html/_sources/core/ui.rst.txt deleted file mode 100644 index 8cfe9283..00000000 --- a/doc_build/_build/html/_sources/core/ui.rst.txt +++ /dev/null @@ -1,143 +0,0 @@ -.. _core_ui: - -.. currentmodules:: pyleoclim.core.ui - -Pyleoclim User API -=================== - -Pyleoclim, like a lot of other Python packages, follows an object-oriented design. It sounds fancy, but it really is `quite simple `_. What this means for you is that we've gone through the trouble of coding up a lot of timeseries analysis methods that apply in various situations - so you don't have to worry about that. -These situations are described in classes, the beauty of which is called "inheritance" (see link above). Basically, it allows to define methods that will automatically apply to your dataset, as long as you put your data within one of those classes. -A major advantage of object-oriented design is that you, the user, can harness the power of Pyleoclim methods in very few lines of code through the user API without ever having to get your hands dirty with our code (unless you want to, of course). -The flipside is that any user would do well to understand Pyleoclim classes, what they are intended for, and what methods they can and cannot support. - -.. image:: Pyleoclim_API.png - :scale: 50 % - :width: 1477px - :height: 946px - :alt: The Pyleoclim User API. Credit: Feng Zhu - :align: center - -The following describes the various classes that undergird the Pyleoclim edifice. - -Series (pyleoclim.Series) -""""""""""""""""""""""""" - -The Series class describes the most basic objects in Pyleoclim. A Series is a simple `dictionary `_ that contains 3 things: -- a series of real-valued numbers; -- a time axis at which those values were measured/simulated ; -- optionally, some metadata about both axes, like units, labels and the like. - -How to create and manipulate such objects is described in a short example below, while `this notebook `_ demonstrates how to apply various Pyleoclim methods to Series objects. - - -.. autoclass:: pyleoclim.core.ui.Series - :members: - - -MultipleSeries (pyleoclim.MultipleSeries) -""""""""""""""""""""""""""""""""""""""""" - -As the name implies, a MultipleSeries object is a collection (more precisely, a `list `_) of multiple Series objects. This is handy in case you want to apply the same method to such a collection at once (e.g. process a bunch of series in a consistent fashion). - -.. autoclass:: pyleoclim.core.ui.MultipleSeries - :members: - - -EnsembleSeries (pyleoclim.EnsembleSeries) -""""""""""""""""""""""""""""""""""""""""" - -The EnsembleSeries class is a child of MultipleSeries, designed for ensemble applications (e.g. draws from a posterior distribution of ages, model ensembles with randomized initial conditions, or some other stochastic ensemble). -Compared to a MultipleSeries object, an EnsembleSeries object has the following properties: [TO BE COMPLETED] - -.. autoclass:: pyleoclim.core.ui.EnsembleSeries - :members: - -SurrogateSeries (pyleoclim.SurrogateSeries) -""""""""""""""""""""""""""""""""""""""""""" - -.. autoclass:: pyleoclim.core.ui.SurrogateSeries - :members: - -Lipd (pyleoclim.Lipd) -""""""""""""""""""""" - -This class allows to manipulate LiPD objects. - -.. autoclass:: pyleoclim.core.ui.Lipd - :members: - - -LipdSeries (pyleoclim.LipdSeries) -""""""""""""""""""""""""""""""""" - -LipdSeries are (you guessed it), Series objects that are created from LiPD objects. As a subclass of Series, they inherit all its methods. -When created, LiPDSeries automatically instantiates the time, value and other parameters from what’s in the lipd file. - -.. autoclass:: pyleoclim.core.ui.LipdSeries - :members: - - -PSD (pyleoclim.PSD) -""""""""""""""""""" - -The PSD (Power spectral density) class is intended for conveniently manipulating the result of spectral methods, including performing significance tests, estimating scaling coefficients, and plotting. -Available methods: - -.. autoclass:: pyleoclim.core.ui.PSD - :members: - -MultiplePSD (pyleoclim.MultiplePSD) -""""""""""""""""""""""""""""""""""" - -.. autoclass:: pyleoclim.core.ui.MultiplePSD - :members: - -Scalogram (pyleoclim.Scalogram) -""""""""""""""""""""""""""""""" -The Scalogram class is analogous to PSD, but for wavelet spectra (scalograms) - -.. autoclass:: pyleoclim.core.ui.Scalogram - :members: - -MultipleScalogram (pyleoclim.MultipleScalogram) -""""""""""""""""""""""""""""""""""""""""""""""" - -.. autoclass:: pyleoclim.core.ui.MultipleScalogram - :members: - -Coherence (pyleoclim.Coherence) -""""""""""""""""""""""""""""""" - -.. autoclass:: pyleoclim.core.ui.Coherence - :members: - -Corr (pyleoclim.Corr) -""""""""""""""""""""" - -.. autoclass:: pyleoclim.core.ui.Corr - :members: - - -CorrEns (pyleoclim.CorrEns) -""""""""""""""""""""""""""" - -.. autoclass:: pyleoclim.core.ui.CorrEns - :members: - -SpatialDecomp (pyleoclim.SpatialDecomp) -""""""""""""""""""""""""""""""""""""""" - -.. autoclass:: pyleoclim.core.ui.SpatialDecomp - :members: - - -SsaRes (pyleoclim.SsaRes) -""""""""""""""""""""""""""" - -.. autoclass:: pyleoclim.core.ui.SsaRes - :members: - -gen_ts (pyleoclim.gen_ts) -""""""""""""""""""""""""" - -.. autofunction:: pyleoclim.gen_ts diff --git a/doc_build/_build/html/_sources/index.rst.txt b/doc_build/_build/html/_sources/index.rst.txt deleted file mode 100644 index b759f5f1..00000000 --- a/doc_build/_build/html/_sources/index.rst.txt +++ /dev/null @@ -1,68 +0,0 @@ -.. Pyleoclim documentation master file, created by - sphinx-quickstart on Fri Feb 10 13:56:30 2017. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Introduction -============ - -Pyleoclim is a Python package designed for the analysis of paleoclimate data. -Pyleoclim leverages various data science libraries (numpy, pandas, scikit-learn) for time series analysis, as well as and Matplotlib and Cartopy for the creation of publication-quality figures. The package is designed around object-oriented :ref:`Series `, which can be directly manipulated for plotting, spectral and wavelet analysis, and other time series-appropriate operations. Basic familiarity with Python is essential, and many good tutorials exist on the topic. - -.. image:: LiPD1p3.png - :width: 191px - :height: 248px - :scale: 100 % - :alt: The LiPD data model, version 1.3. Credit: Nick McKay - :align: right - -Pyleoclim natively "speaks" the language of Linked Paleo Data (`LiPD `_), which enables it to handle most of the data transformations internally, taking a good chunk of the pain out of analyzing paleoclimate data. -The package is aware of age ensembles stored via LiPD and uses them for time-uncertain analysis. Age ensembles can be generated through the `GeoChronR `_ package, which natively stores them as ensemble tables in LiPD. - -While convenient for the representation of paleoclimate observations, LiPD is not the only point of entry into Pyleoclim. The :ref:`Series ` class is very flexible, and allows to apply Pyleoclim functionality to virtually any timeseries, including instrumental or model-generated data, as Excel spreadsheets, numpy arrays or pandas dataframes. Indeed, Pyleoclim is the workhorse supporting more general `machine-learning functionalities `_ for all manner of timeseries. - -Getting Started -=============== - -.. toctree:: - :caption: Working with Pyleoclim - :maxdepth: 1 - - installation.rst - core/ui.rst - tutorials.rst - -The :ref:`Pyleoclim UI ` makes use of specialized routines which are described in details in advanced funtionalities. - -.. toctree:: - :caption: Advanced functionalities - :maxdepth: 1 - - utils/introduction.rst - -Getting Involved -================ - -.. toctree:: - :Hidden: - :caption: Getting Involved - :maxdepth: 2 - - citation.rst - contribution_guide.rst - -Pyleoclim was originally developed to allow scientists to analyze paleoclimate datasets, including visualization, mapping, and time series analysis. Pyleoclim has been made freely available under the terms of the `GNU Public License `_. - -There are many ways to get :ref:`involved in the development of Pyleoclim `: - - * If you write a paper making use of Pyleoclim, please cite it :ref:`thus `. - * Report bugs and problems with the code or documentation to our `GitHub repository `_. Please make sure that there is not outstanding issues that cover the problem you're experiencing. - * Contribute bug fixes - * Contribute enhancements and new features - * Contribute to the code documentation, and share your Pyleoclim-supported scientific workflows via our public repository (`LiPDBooks `_). - -Search Pyleoclim -================ - -* :ref:`genindex` -* :ref:`search` diff --git a/doc_build/_build/html/_sources/installation.rst.txt b/doc_build/_build/html/_sources/installation.rst.txt deleted file mode 100644 index dd02b144..00000000 --- a/doc_build/_build/html/_sources/installation.rst.txt +++ /dev/null @@ -1,128 +0,0 @@ -.. _installation: - -.. note:: - - Pyleoclim requires the use of Python 3.8 or 3.9. - -Installing Pyleoclim -==================== - -We recommend the use of Anaconda or Miniconda, with Pyleoclim setup in -its own `conda` environment. Some default packages shipping with the full Anaconda distribution are known to cause conflicts with the required Pyleoclim packages, so we recommend Miniconda, especially for beginners. - -Installing Anaconda or Miniconda -""""""""""""""""""""""""""""""""" - -To install Anaconda or Miniconda on your platform, follow the instructions from `this page `_. - -Click :ref:`here ` for a quick tutorial on MacOs and Linux systems. - -Creating a new conda environment -""""""""""""""""""""""""""""""""""" - -To create a new environment using Python 3.9 via command line: - -.. code-block:: bash - - conda create -n pyleo python=3.9 - -To view a list of available environment: - -.. code-block:: bash - - conda env list - -To activate your new environment: - -.. code-block:: bash - - conda activate pyleo - -To view the list of packages in your environment: - -.. code-block:: bash - - conda list - -To remove the environment: - -.. code-block:: bash - - conda remove --name pyleo --all - -More information about managing conda environments can be found `here `_. - -Installing Pyleoclim -"""""""""""""""""""" -Make sure that the pyleo environment is activated. - -First install Cartopy: - -.. code-block:: bash - - conda install cartopy - -Then install Pyleoclim through Pypi, which contains the most stable version of Pyleoclim: - -.. code-block:: bash - - pip install pyleoclim - -To install the development version, which contains the most up-to-date features: - -.. code-block:: bash - - pip install git+https://github.com/LinkedEarth/Pyleoclim_util.git@Development - -Note that Pyleoclim is currently affected by `this issue `_, so you -need to use `pip list` to check that the version of `demjson` that was installed is 2.2.4. If it is not, type: - -.. code-block:: bash - - pip install demjson --upgrade - -In some rare cases this may return an error. If so, you first need to downgrade `setuptools`: - -.. code-block:: bash - - pip install setuptools==56.0.0 - -Then upgrade `demjson` as above, and check that the version is 2.2.4 or above. We hope this glitch gets resolved soon! - -If you would like to use Jupyter Notebooks or Spyder for code development, install these packages in your environment: - -.. code-block:: bash - - pip install spyder - pip install jupyter - -.. warning:: - The GUI framework used by the LiPD packages may cause a known conflict with the GUI framework for spyder. If this is the case it is safe to downgrade the conflicting packages. - -.. code-block:: bash - - pip install 'pyqt5<5.13' - pip install 'pyqtwebengine<5.13' - -Building from source for the f2py feature of WWZ -"""""""""""""""""""""""""""""""""""""""""""""""" - -The default version of WWZ that comes with the installation steps mentioned above is relying on `Numba `_. -It is fast enough for lightweight spectral & wavelet analysis tasks, in which case we recommend using the default installation. - -However, it could be slow for heavy use (e.g. performing it for hundreds of times on timeseries with length longer than 1000 points), in which case we recommend activating the f2py feature to achieve an acceleration of around 50%. - -To do that, a Fortran compiler (e.g. :code:`gfortran` or :code:`ifort`) is required on your local machine, and the related Fortran source code should be compiled locally following the steps below: - -- download the source code, either via git clone or just download the .zip file from the `Github repo `_ -- go to the directory :code:`Pyleoclim_util/pyleoclim/f2py`, and then type :code:`make` to compile the .f90 source code with :code:`gfortran` -- one may also edit the :code:`Makefile` to use :code:`ifort` as the compiler to achieve further acceleration; just comment out the line for :code:`gfortran` and use the line for :code:`ifort` below -- a :code:`.so` file will be generated if the compilation is successful -- copy the :code:`.so` file into the directory :code:`Pyleoclim_util/pyleoclim/utils` where Pyleoclim is installed on your machine. To find out the location, one may import the package in Python and "print" it: - -.. code-block:: python - - import pyleoclim as pyleo - print(pyleo) - -Again, unless you are planning to make heavy use of the WWZ functionality, we recommend using the default installation. diff --git a/doc_build/_build/html/_sources/tutorials.rst.txt b/doc_build/_build/html/_sources/tutorials.rst.txt deleted file mode 100644 index ebda11f4..00000000 --- a/doc_build/_build/html/_sources/tutorials.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. tutorials: - -Tutorials -========= - -The main Pyleoclim functionalities are illustrated through this `Jupyter Notebook `_. - -A basic introduction to plotting styles in Pyleoclim is provided in `this notebook `_. - -More advanced paleogeoscientific workflows that leverage LiPD datasets are available as Jupyter notebooks through `LiPDBooks `_. diff --git a/doc_build/_build/html/_sources/utils/causality/granger.rst.txt b/doc_build/_build/html/_sources/utils/causality/granger.rst.txt deleted file mode 100644 index 83d1950a..00000000 --- a/doc_build/_build/html/_sources/utils/causality/granger.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_granger: - -granger_causality (pyleoclim.utils.causality.granger_causality) -===================================== - -.. autofunction:: pyleoclim.utils.causality.granger_causality diff --git a/doc_build/_build/html/_sources/utils/causality/isopersist.rst.txt b/doc_build/_build/html/_sources/utils/causality/isopersist.rst.txt deleted file mode 100644 index d8e7eb9f..00000000 --- a/doc_build/_build/html/_sources/utils/causality/isopersist.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_causality_isopersist: - -signif_isopersist (pyleoclim.utils.causality.signif_isopersist) -===================================== - -.. autofunction:: pyleoclim.utils.causality.signif_isopersist diff --git a/doc_build/_build/html/_sources/utils/causality/isospec.rst.txt b/doc_build/_build/html/_sources/utils/causality/isospec.rst.txt deleted file mode 100644 index bec686d2..00000000 --- a/doc_build/_build/html/_sources/utils/causality/isospec.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_causality_isospec: - -signif_isospec (pyleoclim.utils.causality.signif_isospec) -===================================== - -.. autofunction:: pyleoclim.utils.causality.signif_isospec diff --git a/doc_build/_build/html/_sources/utils/causality/liang.rst.txt b/doc_build/_build/html/_sources/utils/causality/liang.rst.txt deleted file mode 100644 index 78e769ac..00000000 --- a/doc_build/_build/html/_sources/utils/causality/liang.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -.. _utils_liang: - -.. toctree:: - :hidden: - isospec.rst - isopersist.rst - -liang_causality (pyleoclim.utils.causality.liang_causality) -===================================== - -.. autofunction:: pyleoclim.utils.causality.liang_causality diff --git a/doc_build/_build/html/_sources/utils/correlation/corr_isopersist.rst.txt b/doc_build/_build/html/_sources/utils/correlation/corr_isopersist.rst.txt deleted file mode 100644 index 4525f227..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/corr_isopersist.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_corr_isopersist: - -corr_isopersist (pyleoclim.utils.correlation.corr_isopersist) -============================================================= - -.. autofunction:: pyleoclim.utils.correlation.corr_isopersist diff --git a/doc_build/_build/html/_sources/utils/correlation/corr_isospec.rst.txt b/doc_build/_build/html/_sources/utils/correlation/corr_isospec.rst.txt deleted file mode 100644 index de1a94ee..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/corr_isospec.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_corr_isospec: - -corr_isospec (pyleoclim.utils.correlation.corr_isospec) -======================================================= - -.. autofunction:: pyleoclim.utils.correlation.corr_isospec diff --git a/doc_build/_build/html/_sources/utils/correlation/corr_sig.rst.txt b/doc_build/_build/html/_sources/utils/correlation/corr_sig.rst.txt deleted file mode 100644 index 46113839..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/corr_sig.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_corr_sig: - -corr_sig (pyleoclim.utils.correlation.corr_sig) -=================================== - -.. autofunction:: pyleoclim.utils.correlation.corr_sig diff --git a/doc_build/_build/html/_sources/utils/correlation/corr_ttest.rst.txt b/doc_build/_build/html/_sources/utils/correlation/corr_ttest.rst.txt deleted file mode 100644 index 742bb6db..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/corr_ttest.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_corr_ttest: - -corr_ttest (pyleoclim.utils.correlation.corr_ttest) -=================================================== - -.. autofunction:: pyleoclim.utils.correlation.corr_ttest diff --git a/doc_build/_build/html/_sources/utils/correlation/fdr.rst.txt b/doc_build/_build/html/_sources/utils/correlation/fdr.rst.txt deleted file mode 100644 index 9d28c1f3..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/fdr.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_fdr: - -fdr (pyleoclim.utils.correlation.fdr) -========================= - -.. autofunction:: pyleoclim.utils.correlation.fdr diff --git a/doc_build/_build/html/_sources/utils/correlation/fdr_basic.rst.txt b/doc_build/_build/html/_sources/utils/correlation/fdr_basic.rst.txt deleted file mode 100644 index 409b10b6..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/fdr_basic.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_fdr_basic: - -fdr_basic (pyleoclim.utils.correlation.fdr_basic) -================================================= - -.. autofunction:: pyleoclim.utils.correlation.fdr_basic diff --git a/doc_build/_build/html/_sources/utils/correlation/fdr_master.rst.txt b/doc_build/_build/html/_sources/utils/correlation/fdr_master.rst.txt deleted file mode 100644 index ee6a6e24..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/fdr_master.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_fdr_master: - -fdr_master (pyleoclim.utils.correlation.fdr_master) -=================================================== - -.. autofunction:: pyleoclim.utils.correlation.fdr_master diff --git a/doc_build/_build/html/_sources/utils/correlation/isopersistent_rn.rst.txt b/doc_build/_build/html/_sources/utils/correlation/isopersistent_rn.rst.txt deleted file mode 100644 index 735b251d..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/isopersistent_rn.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_isopersistent_rn: - -isopersistent_rn (pyleoclim.utils.correlation.isopersistent_rn) -=============================================================== - -.. autofunction:: pyleoclim.utils.correlation.isopersistent_rn diff --git a/doc_build/_build/html/_sources/utils/correlation/phaseran.rst.txt b/doc_build/_build/html/_sources/utils/correlation/phaseran.rst.txt deleted file mode 100644 index a149dccf..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/phaseran.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_phaseran: - -phaseran (pyleoclim.utils.correlation.phaseran) -================================================= - -.. autofunction:: pyleoclim.utils.correlation.phaseran diff --git a/doc_build/_build/html/_sources/utils/correlation/prop_alt.rst.txt b/doc_build/_build/html/_sources/utils/correlation/prop_alt.rst.txt deleted file mode 100644 index 68fbca15..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/prop_alt.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_prop_alt: - -prop_alt (pyleoclim.utils.correlation.prop_alt) -=============================================== - -.. autofunction:: pyleoclim.utils.correlation.prop_alt diff --git a/doc_build/_build/html/_sources/utils/correlation/red_noise.rst.txt b/doc_build/_build/html/_sources/utils/correlation/red_noise.rst.txt deleted file mode 100644 index 68a3aaba..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/red_noise.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_red_noise: - -red_noise (pyleoclim.utils.correlation.red_noise) -================================================= - -.. autofunction:: pyleoclim.utils.correlation.red_noise diff --git a/doc_build/_build/html/_sources/utils/correlation/sm_ar1_fit.rst.txt b/doc_build/_build/html/_sources/utils/correlation/sm_ar1_fit.rst.txt deleted file mode 100644 index 95b7eb2e..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/sm_ar1_fit.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_sm_ar1_fit: - -sm_ar1_fit (pyleoclim.utils.correlation.sm_ar1_fit) -=================================================== - -.. autofunction:: pyleoclim.utils.correlation.sm_ar1_fit diff --git a/doc_build/_build/html/_sources/utils/correlation/sm_ar1_sim.rst.txt b/doc_build/_build/html/_sources/utils/correlation/sm_ar1_sim.rst.txt deleted file mode 100644 index a2caad29..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/sm_ar1_sim.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_sm_ar1_sim: - -sm_ar1_sim (pyleoclim.utils.correlation.sm_ar1_sim) -=================================================== - -.. autofunction:: pyleoclim.utils.correlation.sm_ar1_sim diff --git a/doc_build/_build/html/_sources/utils/correlation/storey.rst.txt b/doc_build/_build/html/_sources/utils/correlation/storey.rst.txt deleted file mode 100644 index b08e60de..00000000 --- a/doc_build/_build/html/_sources/utils/correlation/storey.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_correlation_storey: - -storey (pyleoclim.utils.correlation.storey) -=========================================== - -.. autofunction:: pyleoclim.utils.correlation.storey diff --git a/doc_build/_build/html/_sources/utils/decomposition/mpca.rst.txt b/doc_build/_build/html/_sources/utils/decomposition/mpca.rst.txt deleted file mode 100644 index 2e8244d0..00000000 --- a/doc_build/_build/html/_sources/utils/decomposition/mpca.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_mpca: - -mpca (pyleoclim.utils.decomposition.mpca) -========================================= - -.. autofunction:: pyleoclim.utils.decomposition.mpca diff --git a/doc_build/_build/html/_sources/utils/decomposition/mssa.rst.txt b/doc_build/_build/html/_sources/utils/decomposition/mssa.rst.txt deleted file mode 100644 index 48dd8f09..00000000 --- a/doc_build/_build/html/_sources/utils/decomposition/mssa.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_mssa: - -mssa (pyleoclim.utils.decomposition.mssa) -===================================== - -.. autofunction:: pyleoclim.utils.decomposition.mssa diff --git a/doc_build/_build/html/_sources/utils/decomposition/ssa.rst.txt b/doc_build/_build/html/_sources/utils/decomposition/ssa.rst.txt deleted file mode 100644 index 835b44a3..00000000 --- a/doc_build/_build/html/_sources/utils/decomposition/ssa.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_ssa: - -ssa (pyleoclim.utils.decompoition.ssa) -===================================== - -.. autofunction:: pyleoclim.utils.decomposition.ssa diff --git a/doc_build/_build/html/_sources/utils/filter/butterworth.rst.txt b/doc_build/_build/html/_sources/utils/filter/butterworth.rst.txt deleted file mode 100644 index 1e662066..00000000 --- a/doc_build/_build/html/_sources/utils/filter/butterworth.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_butterworth: - -butterworth (pyleoclim.utils.filter.butterworth) -===================================== - -.. autofunction:: pyleoclim.utils.filter.butterworth diff --git a/doc_build/_build/html/_sources/utils/filter/firwin.rst.txt b/doc_build/_build/html/_sources/utils/filter/firwin.rst.txt deleted file mode 100644 index a9faaab9..00000000 --- a/doc_build/_build/html/_sources/utils/filter/firwin.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_firwin: - -firwin (pyleoclim.utils.filter.firwin) -====================================== - -.. autofunction:: pyleoclim.utils.filter.firwin diff --git a/doc_build/_build/html/_sources/utils/filter/lanczos.rst.txt b/doc_build/_build/html/_sources/utils/filter/lanczos.rst.txt deleted file mode 100644 index 832602c7..00000000 --- a/doc_build/_build/html/_sources/utils/filter/lanczos.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_lanczos: - -lanczos (pyleoclim.utils.filter.lanczos) -======================================= - -.. autofunction:: pyleoclim.utils.filter.lanczos diff --git a/doc_build/_build/html/_sources/utils/filter/savitzky_golay.rst.txt b/doc_build/_build/html/_sources/utils/filter/savitzky_golay.rst.txt deleted file mode 100644 index 42ab0003..00000000 --- a/doc_build/_build/html/_sources/utils/filter/savitzky_golay.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_savitzky_golay: - -savitzky_golay (pyleoclim.utils.filter.savitzky_golay) -===================================== - -.. autofunction:: pyleoclim.utils.filter.savitzky_golay diff --git a/doc_build/_build/html/_sources/utils/filter/ts_pad.rst.txt b/doc_build/_build/html/_sources/utils/filter/ts_pad.rst.txt deleted file mode 100644 index e6099b14..00000000 --- a/doc_build/_build/html/_sources/utils/filter/ts_pad.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_filter_ts_pad: - -ts_pad (pyleoclim.utils.filter.ts_pad) -=========================================== - -.. autofunction:: pyleoclim.utils.filter.ts_pad diff --git a/doc_build/_build/html/_sources/utils/introduction.rst.txt b/doc_build/_build/html/_sources/utils/introduction.rst.txt deleted file mode 100644 index 2e420bb1..00000000 --- a/doc_build/_build/html/_sources/utils/introduction.rst.txt +++ /dev/null @@ -1,249 +0,0 @@ -.. _utils_introduction: - -Pyleoclim Utilities API (pyleoclim.utils) -========================================= - -Pyleoclim makes extensive use of functions from `numpy `_, `Pandas `_, `Scipy `_, and `scikit-learn `_. Please note that some default parameter values for these functions have been changed to more appropriate values for paleoclimate datasets. - -Causality -""""""""" -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`granger_causality ` - - Estimate Granger causality - * - :ref:`liang_causality ` - - Estimate Liang causality - -Correlation -""""""""""" - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`corr_sig ` - - Estimates the Pearson's correlation and associated significance between two time series, applicable to cases where the standard assumption of independence breaks down. Three methods are currently implemented: t test with a heuristic correction for the degrees of freedom, Monte Carlo simulations based on an AR(1) model (`isopersist`), and phase randomization (`isospectral`). - * - :ref:`fdr ` - - False Discovery Rate, as per the method of Benjamini and Hochberg [1995] - - -Decomposition -""""""""""""" - -Methods used for decomposing timeseries into orthogonal components. - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`mpca ` - - Monte-Carlo Principal Component Analysis (PCA, sometimes known as EOF analysis) - * - :ref:`ssa ` - - Singular Spectrum Analysis - * - :ref:`MSSA ` - - Multi Channel Singular Spectrum Analysis. - -Filter -"""""" - -Filtering functions - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`Savitzky-Golay filter ` - - Smooth (and optionally differentiate) data with a Savitzky-Golay filter - * - :ref:`Butterworth filter ` - - Applies a Butterworth filter with frequency fc, with optional padding - * - :ref:`firwin filter ` - - Applies a Finite Impulse Response filter design with window method and frequency fc, with padding - * - :ref:`lanczos filter ` - - Applies a Lanczos (lowpass) filter with frequency fc, with optional padding - -Mapping -""""""" - -This module contains mapping function based on `cartopy _` - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`map_all ` - - Maps records according to some criteria (e.g, proxy type, interpretation) - -Plotting -"""""""" - -The functions contained in this module rely heavily on `matplotlib _`. See :ref:`here ` for details. If considering plotting without making use of the functions in the ui module, we recommend using matplotlib directly. - -However, the following functions can be used to manipulate the default style and save settings. - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`showfig ` - - Shows the figure - * - :ref:`savefig ` - - Saves the figure to a user specified path - * - :ref:`closefig ` - - Closes the figure - * - :ref:`set_style ` - - Modifies the visualization style - -Spectral -"""""""" - -This modules contains several spectral methods applicable to paleoclimate data - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`welch ` - - Estimate power spectral density using Welch's method - * - :ref:`periodogram ` - - Estimate power spectral density using periodogram method - * - :ref:`mtm ` - - Estimate power spectral density using multi-taper method - * - :ref:`lomb_scargle ` - - Estimate power spectral density using the Lomb-Scargle method - * - :ref:`wwz_psd ` - - Estimate power spectral density using the Weighted Z-Transform wavelet method - -Tsmodel -""""""" - -This module generates simulated time series that can be used for significance testing. - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`ar1_sim ` - - Produces p realizations of an AR(1) process of length n with lag-1 autocorrelation g calculated from `y` and (if provided) `t` - * - :ref:`colored_noise ` - - Generate a colored noise with given scaling factor `alpha` - * - :ref:`colored_noise_2regimes ` - - Generate a colored noise with two regimes given scaling factors `alpha1` and `alpha2` - * - :ref:`gen_ar1_evenly ` - - Generate AR(1) series samples - -Wavelet -""""""" - -Functions for wavelet analysis. Includes some pre-processing and post-processing functions for spectral and wavelet analysis described :ref:`here `. - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`wwz ` - - Weighted wavelet amplitude (WWA) for unevenly-spaced data - * - :ref:`xwc ` - - Cross-wavelet analysis for unevenly-spaced data. - - -Tsutils -""""""" - -This modules contain pre-processing functions for time series analysis. - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`simple_stats ` - - Computes the mean, median, min, max, standard deviation and interquartile range of a timeseries - * - :ref:`bin ` - - Bin the values into evenly-spaced bins - * - :ref:`gkernel ` - - Coarsen time resolution using a Gaussian Kernel - * - :ref:`grid_properties ` - - Establishes the grid properties of a numerical array - * - :ref:`interp ` - - Interpolation function based on `scipy.interpolate.interp1d _` - * - :ref:`on_common_axis ` - - Places two timeseries on a common time axis - * - :ref:`standardize ` - - Standardizes a timeseries - * - :ref:`ts2segments ` - - Chop a timeseries into several segments based on gap detection - * - :ref:`annualize ` - - Annualize a time series whose time resolution is finer than 1 year - * - :ref:`gaussianize ` - - Maps a (proxy) timeseries to a Gaussian distribution - * - :ref:`gaussianize_single ` - - Transforms a single (proxy) timeseries to a Gaussian distribution - * - :ref:`detrend ` - - Applies linear, constant, low-pass filter, or decomposition-based detrending - * - :ref:`detect_outliers ` - - Detect outliers in a timeseries - * - :ref:`remove_outliers ` - - Remove outliers in a timeseries - - -Tsbase -"""""" - -This module contains simple cleaning routines. - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`clean_ts ` - - Remove NaNs in the time series and sort it in ascending time order - * - :ref:`dropna ` - - Remove NaNs - * - :ref:`sort_ts ` - - Sort time values in ascending order - * - :ref:`reduce_duplicated_timestamps ` - - Reduce duplicated timestamps in a timeseries by averaging the values - * - :ref:`is_evenly_spaced ` - - Detect whether a timeseries is evenly spaced in time - -Lipdutils -""""""""" -This module contains functions to manipulate LiPD files and automate data transformation whenever possible. These functions are used throughout Pyleoclim but are not meant for direct interactions. A list of these functions can be found :ref:`here `. - -The most relevant functions concern querying the LinkedEarth wiki. The first 5 functions can be used to get relevant query terms. - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`whatArchives ` - - Query the names of all ArchiveTypes from the LinkedEarth Ontology - * - :ref:`whatProxyObservations ` - - Query the names of all ProxyObservations from the LinkedEarth Ontology - * - :ref:`whatProxySensors ` - - Query the names of all ProxySensors from the LinkedEarth Ontology - * - :ref:`whatInferredVariables ` - - Query the names of all InferredVariables from the LinkedEarth Ontology - * - :ref:`whatInterpretations ` - - Query the names of all Interpretations from the LinkedEarth Ontology. - * - :ref:`queryLinkedEarth ` - - Query the LinkedEarth wiki for datasets. - -jsonutils -""""""""" - -This module converts Pyleoclim objects to and from JSON files. Useful for obtaining a human-readable output and keeping the results of an analysis. - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`PyleoObj_to_json ` - - Saves a Pyleoclim Object (e.g., Series, PSD, Scalogram) to a json file - * - :ref:`json_to_Series ` - - Load a pyleoclim Series object from a JSON file - * - :ref:`json_to_PSD ` - - Load a pyleoclim PSD object from a JSON file - * - :ref:`json_to_Scalogram ` - - Load a pyleoclim Scalogram object from a JSON file diff --git a/doc_build/_build/html/_sources/utils/jsonutils/PyleoObj_to_json.rst.txt b/doc_build/_build/html/_sources/utils/jsonutils/PyleoObj_to_json.rst.txt deleted file mode 100644 index 8bd1a9e3..00000000 --- a/doc_build/_build/html/_sources/utils/jsonutils/PyleoObj_to_json.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_PyleoObj_to_json: - -PyleoObj_to_json (pyleoclim.utils.jsonutils.PyleoObj_to_json) -============================================================= - -.. autofunction:: pyleoclim.utils.jsonutils.PyleoObj_to_json diff --git a/doc_build/_build/html/_sources/utils/jsonutils/json_to_PSD.rst.txt b/doc_build/_build/html/_sources/utils/jsonutils/json_to_PSD.rst.txt deleted file mode 100644 index 0bf83790..00000000 --- a/doc_build/_build/html/_sources/utils/jsonutils/json_to_PSD.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_json_to_PSD: - -json_to_PSD (pyleoclim.utils.jsonutils.json_to_PSD) -=================================================== - -.. autofunction:: pyleoclim.utils.jsonutils.json_to_PSD diff --git a/doc_build/_build/html/_sources/utils/jsonutils/json_to_Scalogram.rst.txt b/doc_build/_build/html/_sources/utils/jsonutils/json_to_Scalogram.rst.txt deleted file mode 100644 index c866a773..00000000 --- a/doc_build/_build/html/_sources/utils/jsonutils/json_to_Scalogram.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_json_to_Scalogram: - -json_to_Scalogram (pyleoclim.utils.jsonutils.json_to_Scalogram) -=============================================================== - -.. autofunction:: pyleoclim.utils.jsonutils.json_to_Scalogram diff --git a/doc_build/_build/html/_sources/utils/jsonutils/json_to_Series.rst.txt b/doc_build/_build/html/_sources/utils/jsonutils/json_to_Series.rst.txt deleted file mode 100644 index 87533ee9..00000000 --- a/doc_build/_build/html/_sources/utils/jsonutils/json_to_Series.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_json_to_Series: - -json_to_Series (pyleoclim.utils.jsonutils.json_to_Series) -========================================================= - -.. autofunction:: pyleoclim.utils.jsonutils.json_to_Series diff --git a/doc_build/_build/html/_sources/utils/lipdutils/LipdToOntology.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/LipdToOntology.rst.txt deleted file mode 100644 index c6b7d7d4..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/LipdToOntology.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_LipdToOntology: - -LipdToOntology (pyleoclim.utils.lipdutils.LipdToOntology) -========================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.LipdToOntology diff --git a/doc_build/_build/html/_sources/utils/lipdutils/checkTimeAxis.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/checkTimeAxis.rst.txt deleted file mode 100644 index d8c95f07..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/checkTimeAxis.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_checkTimeAxis: - -checkTimeAxis (pyleoclim.utils.lipdutils.checkTimeAxis) -======================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.checkTimeAxis diff --git a/doc_build/_build/html/_sources/utils/lipdutils/checkXaxis.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/checkXaxis.rst.txt deleted file mode 100644 index 81be4471..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/checkXaxis.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_checkXaxis: - -checkXaxis (pyleoclim.utils.lipdutils.checkXaxis) -================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.checkXaxis diff --git a/doc_build/_build/html/_sources/utils/lipdutils/enumerateLipds.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/enumerateLipds.rst.txt deleted file mode 100644 index 03df747a..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/enumerateLipds.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_enumerateLipds: - -enumerateLipds (pyleoclim.utils.lipdutils.enumerateLipds) -========================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.enumerateLipds diff --git a/doc_build/_build/html/_sources/utils/lipdutils/enumerateTs.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/enumerateTs.rst.txt deleted file mode 100644 index c8788585..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/enumerateTs.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_enumerateTs: - -enumerateTs (pyleoclim.utils.lipdutils.enumerateTs) -=================================================== - -.. autofunction:: pyleoclim.utils.lipdutils.enumerateTs diff --git a/doc_build/_build/html/_sources/utils/lipdutils/gen_dict_extract.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/gen_dict_extract.rst.txt deleted file mode 100644 index 0208a885..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/gen_dict_extract.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_gen_dict_extract: - -gen_dict_extract (pyleoclim.utils.lipdutils.gen_dict_extract) -============================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.gen_dict_extract diff --git a/doc_build/_build/html/_sources/utils/lipdutils/getEnsemble.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/getEnsemble.rst.txt deleted file mode 100644 index d9270c2a..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/getEnsemble.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_getEnsemble: - -getEnsemble (pyleoclim.utils.lipdutils.getEnsemble) -=================================================== - -.. autofunction:: pyleoclim.utils.lipdutils.getEnsemble diff --git a/doc_build/_build/html/_sources/utils/lipdutils/getLipd.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/getLipd.rst.txt deleted file mode 100644 index 4dd3d8c8..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/getLipd.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_getLipd: - -getLipd (pyleoclim.utils.lipdutils.getLipd) -=========================================== - -.. autofunction:: pyleoclim.utils.lipdutils.getLipd diff --git a/doc_build/_build/html/_sources/utils/lipdutils/getMeasurement.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/getMeasurement.rst.txt deleted file mode 100644 index af52331d..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/getMeasurement.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_getMeasurement: - -getMeasurement (pyleoclim.utils.lipdutils.getMeasurement) -=========================================================== - -.. autofunction:: pyleoclim.utils.lipdutils.getMeasurement diff --git a/doc_build/_build/html/_sources/utils/lipdutils/getTs.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/getTs.rst.txt deleted file mode 100644 index f764cf5b..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/getTs.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_getTs: - -getTs (pyleoclim.utils.lipdutils.getTs) -======================================= - -.. autofunction:: pyleoclim.utils.lipdutils.getTs diff --git a/doc_build/_build/html/_sources/utils/lipdutils/isEnsemble.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/isEnsemble.rst.txt deleted file mode 100644 index dd7d52a1..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/isEnsemble.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_isEnsemble: - -isEnsemble (pyleoclim.utils.lipdutils.isEnsemble) -================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.isEnsemble diff --git a/doc_build/_build/html/_sources/utils/lipdutils/isMeasurement.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/isMeasurement.rst.txt deleted file mode 100644 index e13bc650..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/isMeasurement.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_isMeasurement: - -isMeasurement (pyleoclim.utils.lipdutils.isMeasurement) -======================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.isMeasurement diff --git a/doc_build/_build/html/_sources/utils/lipdutils/isModel.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/isModel.rst.txt deleted file mode 100644 index 1bf9f448..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/isModel.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_isModel: - -isModel (pyleoclim.utils.lipdutils.isModel) -=========================================== - -.. autofunction:: pyleoclim.utils.lipdutils.isModel diff --git a/doc_build/_build/html/_sources/utils/lipdutils/mapAgeEnsembleToPaleoData.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/mapAgeEnsembleToPaleoData.rst.txt deleted file mode 100644 index 92691810..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/mapAgeEnsembleToPaleoData.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_mapAgeEnsembleToPaleoData: - -mapAgeEnsembleToPaleoData (pyleoclim.utils.lipdutils.mapAgeEnsembleToPaleoData) -=============================================================================== - -.. autofunction:: pyleoclim.utils.lipdutils.mapAgeEnsembleToPaleoData diff --git a/doc_build/_build/html/_sources/utils/lipdutils/modelNumber.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/modelNumber.rst.txt deleted file mode 100644 index 68190594..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/modelNumber.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_modelNumber: - -modelNumber (pyleoclim.utils.lipdutils.modelNumber) -=================================================== - -.. autofunction:: pyleoclim.utils.lipdutils.modelNumber diff --git a/doc_build/_build/html/_sources/utils/lipdutils/pre_process_list.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/pre_process_list.rst.txt deleted file mode 100644 index 3e5ade02..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/pre_process_list.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_pre_process_list: - -pre_process_list (pyleoclim.utils.lipdutils.pre_process_list) -============================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.pre_process_list diff --git a/doc_build/_build/html/_sources/utils/lipdutils/pre_process_str.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/pre_process_str.rst.txt deleted file mode 100644 index 05d00e37..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/pre_process_str.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_pre_process_str: - -pre_process_str (pyleoclim.utils.lipdutils.pre_process_str) -=========================================================== - -.. autofunction:: pyleoclim.utils.lipdutils.pre_process_str diff --git a/doc_build/_build/html/_sources/utils/lipdutils/private.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/private.rst.txt deleted file mode 100644 index 02d65dc8..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/private.rst.txt +++ /dev/null @@ -1,84 +0,0 @@ -.. _lipdutils_private: - -.. toctree:: - :hidden: - checkTimeAxis.rst - checkXaxis.rst - enumerateLipds.rst - enumerateTs.rst - gen_dict_extract.rst - getEnsemble.rst - getLipd.rst - getMeasurement.rst - getTs.rst - isEnsemble.rst - isMeasurement.rst - isModel.rst - LipdToOntology.rst - pre_process_list.rst - pre_process_str.rst - promptForVariable.rst - searchVar.rst - similar_string.rst - timeUnitsCheck.rst - whichEnsemble.rst - whichMeasurement.rst - xAxisTs.rst - -LiPD Utilities (pyleoclim.utils.lipdutils) -========================================== - -Pyleoclim is meant to directly handle datasets in the Linked Paleo Data (`LiPD `_) format. Pyleoclim works with timeseries objects and model tables present in these files. - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`enumerateLipds ` - - enumerate the LiPD files loaded in the workspace - * - :ref:`getLipd ` - - Prompt for a LiPD files - * - :ref:`promptForVariable ` - - Prompt for a specific variable - * - :ref:`xAxisTs ` - - Get the x-axis for the timeseries - * - :ref:`checkXaxis ` - - Check that a x-axis is present for the timeseries - * - :ref:`checkTimeAxis ` - - This function makes sure that time is available for the timeseries - * - :ref:`searchVar ` - - This functions searches for keywords (exact match) for a variable. - * - :ref:`enumerateTs ` - - Enumerate the available time series objects - * - :ref:`getTs ` - - Get a specific timeseries object from a dictionary of timeseries - * - :ref:`LipdToOntology ` - - Standardize archiveType - * - :ref:`timeUnitsCheck ` - - This function attempts to make sense of the time units by checking for equivalence - * - :ref:`pre_process_list ` - - Pre-process a series of strings for capitalized letters, space, and punctuation. - * - :ref:`similar_string ` - - Returns a list of indices for strings with similar values - * - :ref:`pre_process_str ` - - Pre-process a string for capitalized letters, space, and punctuation - * - :ref:`isModel ` - - Check for the presence of a model in the same object as the measurement table - * - :ref:`modelNumber ` - - Assign a new or existing model number - * - :ref:`isMeasurement ` - - Check whether measurement tables are available - * - :ref:`whichMeasurement ` - - Select a measurement table from a list - * - :ref:`getMeasurement ` - - Extract the dictionary corresponding to the measurement table - * - :ref:`isEnsemble ` - - Check whether ensembles are available - * - :ref:`whichEnsemble ` - - Select an ensemble table from a list - * - :ref:`getEnsemble ` - - Extracts the ensemble values and depth vector from the dictionary - * - :ref:`mapAgeEnsembleToPaleoData ` - - Map the depth for the ensemble age values to the paleo depth - * - :ref:`gen_dict_extract ` - - Recursively searches for all the values in nested dictionaries corresponding to a particular key diff --git a/doc_build/_build/html/_sources/utils/lipdutils/promptForVariable.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/promptForVariable.rst.txt deleted file mode 100644 index 32f4f30a..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/promptForVariable.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_promptForVariable: - -promptForVariable (pyleoclim.utils.lipdutils.promptForVariable) -=============================================================== - -.. autofunction:: pyleoclim.utils.lipdutils.promptForVariable diff --git a/doc_build/_build/html/_sources/utils/lipdutils/queryLinkedEarth.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/queryLinkedEarth.rst.txt deleted file mode 100644 index b5b7d39b..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/queryLinkedEarth.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_queryLinkedEarth: - -queryLinkedEarth (pyleoclim.utils.lipdutils.queryLinkedEarth) -=============================================== - -.. autofunction:: pyleoclim.utils.lipdutils.queryLinkedEarth diff --git a/doc_build/_build/html/_sources/utils/lipdutils/searchVar.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/searchVar.rst.txt deleted file mode 100644 index 07e5a890..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/searchVar.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_searchVar: - -searchVar (pyleoclim.utils.lipdutils.searchVar) -=============================================== - -.. autofunction:: pyleoclim.utils.lipdutils.searchVar diff --git a/doc_build/_build/html/_sources/utils/lipdutils/similar_string.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/similar_string.rst.txt deleted file mode 100644 index 5c34fb52..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/similar_string.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_similar_string: - -similar_string (pyleoclim.utils.lipdutils.similar_string) -======================================================== - -.. autofunction:: pyleoclim.utils.lipdutils.similar_string diff --git a/doc_build/_build/html/_sources/utils/lipdutils/timeUnitsCheck.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/timeUnitsCheck.rst.txt deleted file mode 100644 index eecabe28..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/timeUnitsCheck.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_timeUnitsCheck: - -timeUnitsCheck (pyleoclim.utils.lipdutils.timeUnitsCheck) -========================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.timeUnitsCheck diff --git a/doc_build/_build/html/_sources/utils/lipdutils/whatArchives.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/whatArchives.rst.txt deleted file mode 100644 index b25a07e4..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/whatArchives.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_whatArchives: - -whatArchives (pyleoclim.utils.lipdutils.whatArchives) -=========================================== - -.. autofunction:: pyleoclim.utils.lipdutils.whatArchives diff --git a/doc_build/_build/html/_sources/utils/lipdutils/whatInferredVariables.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/whatInferredVariables.rst.txt deleted file mode 100644 index 0f03439f..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/whatInferredVariables.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_whatInferredVariables: - -whatInferredVariables (pyleoclim.utils.lipdutils.whatInferredVariables) -============================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.whatInferedVariables diff --git a/doc_build/_build/html/_sources/utils/lipdutils/whatInterpretations.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/whatInterpretations.rst.txt deleted file mode 100644 index 76ac4dec..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/whatInterpretations.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_whatInterpretations: - -whatInterpretations (pyleoclim.utils.lipdutils.whatInterpretations) -========================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.whatInterpretations diff --git a/doc_build/_build/html/_sources/utils/lipdutils/whatProxyObservations.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/whatProxyObservations.rst.txt deleted file mode 100644 index 16e76592..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/whatProxyObservations.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_whatProxyObservations: - -whatProxyObservations (pyleoclim.utils.lipdutils.whatProxyObservations) -============================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.whatProxyObservations diff --git a/doc_build/_build/html/_sources/utils/lipdutils/whatProxySensors.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/whatProxySensors.rst.txt deleted file mode 100644 index 6410d1c1..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/whatProxySensors.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_whatProxySensors: - -whatproxySensors (pyleoclim.utils.lipdutils.whatProxySensors) -=================================================== - -.. autofunction:: pyleoclim.utils.lipdutils.whatProxySensors diff --git a/doc_build/_build/html/_sources/utils/lipdutils/whichEnsemble.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/whichEnsemble.rst.txt deleted file mode 100644 index 17a09084..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/whichEnsemble.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_whichEnsemble: - -whichEnsemble (pyleoclim.utils.lipdutils.whichEnsemble) -======================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.whichEnsemble diff --git a/doc_build/_build/html/_sources/utils/lipdutils/whichMeasurement.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/whichMeasurement.rst.txt deleted file mode 100644 index e179889a..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/whichMeasurement.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_whichMeasurement: - -whichMeasurement (pyleoclim.utils.lipdutils.whichMeasurement) -============================================================= - -.. autofunction:: pyleoclim.utils.lipdutils.whichMeasurement diff --git a/doc_build/_build/html/_sources/utils/lipdutils/xAxisTs.rst.txt b/doc_build/_build/html/_sources/utils/lipdutils/xAxisTs.rst.txt deleted file mode 100644 index cc8aec36..00000000 --- a/doc_build/_build/html/_sources/utils/lipdutils/xAxisTs.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _lipdutils_xAxisTs: - -xAxisTs (pyleoclim.utils.lipdutils.xAxisTs) -=========================================== - -.. autofunction:: pyleoclim.utils.lipdutils.xAxisTs diff --git a/doc_build/_build/html/_sources/utils/mapping/compute_dist.rst.txt b/doc_build/_build/html/_sources/utils/mapping/compute_dist.rst.txt deleted file mode 100644 index a4aaa049..00000000 --- a/doc_build/_build/html/_sources/utils/mapping/compute_dist.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_mapping_computedist: - -compute_dist (pyleoclim.utils.mapping.compute_dist) -=================================================== - -.. autofunction:: pyleoclim.utils.mapping.compute_dist diff --git a/doc_build/_build/html/_sources/utils/mapping/dist_sphere.rst.txt b/doc_build/_build/html/_sources/utils/mapping/dist_sphere.rst.txt deleted file mode 100644 index e38dcb17..00000000 --- a/doc_build/_build/html/_sources/utils/mapping/dist_sphere.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_mapping_distsphere: - -dist_sphere (pyleoclim.utils.mapping.dist_sphere) -================================================= - -.. autofunction:: pyleoclim.utils.mapping.dist_sphere diff --git a/doc_build/_build/html/_sources/utils/mapping/map_all.rst.txt b/doc_build/_build/html/_sources/utils/mapping/map_all.rst.txt deleted file mode 100644 index b562b62f..00000000 --- a/doc_build/_build/html/_sources/utils/mapping/map_all.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_mapall: - -map_all (pyleoclim.utils.mapping.map_all) -================================= - -.. autofunction:: pyleoclim.utils.mapping.map_all diff --git a/doc_build/_build/html/_sources/utils/mapping/set_proj.rst.txt b/doc_build/_build/html/_sources/utils/mapping/set_proj.rst.txt deleted file mode 100644 index 62a14031..00000000 --- a/doc_build/_build/html/_sources/utils/mapping/set_proj.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_mapping_setproj: - -set_proj (pyleoclim.utils.mapping.set_proj) -=========================================== - -.. autofunction:: pyleoclim.utils.mapping.set_proj diff --git a/doc_build/_build/html/_sources/utils/mapping/within_distance.rst.txt b/doc_build/_build/html/_sources/utils/mapping/within_distance.rst.txt deleted file mode 100644 index 548134c8..00000000 --- a/doc_build/_build/html/_sources/utils/mapping/within_distance.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_mapping_withindistance: - -within_distance (pyleoclim.utils.mapping.within_distance) -========================================================= - -.. autofunction:: pyleoclim.utils.mapping.within_distance diff --git a/doc_build/_build/html/_sources/utils/plotting/closefig.rst.txt b/doc_build/_build/html/_sources/utils/plotting/closefig.rst.txt deleted file mode 100644 index fa8adaf0..00000000 --- a/doc_build/_build/html/_sources/utils/plotting/closefig.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_closefig: - -closefig (pyleoclim.utils.plotting.closefig) -============================================ - -.. autofunction:: pyleoclim.utils.plotting.closefig diff --git a/doc_build/_build/html/_sources/utils/plotting/in_notebook.rst.txt b/doc_build/_build/html/_sources/utils/plotting/in_notebook.rst.txt deleted file mode 100644 index dfe8b263..00000000 --- a/doc_build/_build/html/_sources/utils/plotting/in_notebook.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _plotting_in_notebook: - -in_notebook (pyleoclim.utils.plotting.in_notebook) -================================================== - -.. autofunction:: pyleoclim.utils.plotting.in_notebook diff --git a/doc_build/_build/html/_sources/utils/plotting/plot_scatter_xy.rst.txt b/doc_build/_build/html/_sources/utils/plotting/plot_scatter_xy.rst.txt deleted file mode 100644 index 5896f833..00000000 --- a/doc_build/_build/html/_sources/utils/plotting/plot_scatter_xy.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _plotting_plot_scatter_xy: - -plot_scatter_xy (pyleoclim.utils.plotting.plot_scatter_xy) -========================================================== - -.. autofunction:: pyleoclim.utils.plotting.plot_scatter_xy diff --git a/doc_build/_build/html/_sources/utils/plotting/plot_xy.rst.txt b/doc_build/_build/html/_sources/utils/plotting/plot_xy.rst.txt deleted file mode 100644 index d2d93cda..00000000 --- a/doc_build/_build/html/_sources/utils/plotting/plot_xy.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _plotting_plot_xy: - -plot_xy (pyleoclim.utils.plotting.plot_xy) -========================================== - -.. autofunction:: pyleoclim.utils.plotting.plot_xy diff --git a/doc_build/_build/html/_sources/utils/plotting/private.rst.txt b/doc_build/_build/html/_sources/utils/plotting/private.rst.txt deleted file mode 100644 index 353d5fee..00000000 --- a/doc_build/_build/html/_sources/utils/plotting/private.rst.txt +++ /dev/null @@ -1,23 +0,0 @@ -.. _plotting_private: - -.. toctree:: - :hidden: - plot_scatter_xy.rst - plot_xy.rst - stackplot.rst - -Plotting (pyleoclim.utils.plotting) -=================================== - -List of plotting functions internal to Pyleoclim. - -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`plot_scatter_xy ` - - Plots a scatter plot on top of a line plot - * - :ref:`plot_xy ` - - Basic line plot - * - :ref:`stackplot ` - - Stackplot diff --git a/doc_build/_build/html/_sources/utils/plotting/savefig.rst.txt b/doc_build/_build/html/_sources/utils/plotting/savefig.rst.txt deleted file mode 100644 index e4c8bc42..00000000 --- a/doc_build/_build/html/_sources/utils/plotting/savefig.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_savefig: - -savefig (pyleoclim.utils.plotting.savefig) -================================= - -.. autofunction:: pyleoclim.utils.plotting.savefig diff --git a/doc_build/_build/html/_sources/utils/plotting/set_style.rst.txt b/doc_build/_build/html/_sources/utils/plotting/set_style.rst.txt deleted file mode 100644 index c220b9fb..00000000 --- a/doc_build/_build/html/_sources/utils/plotting/set_style.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_set_style: - -set_style (pyleoclim.utils.plotting.set_style) -===================================== - -.. autofunction:: pyleoclim.utils.plotting.set_style diff --git a/doc_build/_build/html/_sources/utils/plotting/showfig.rst.txt b/doc_build/_build/html/_sources/utils/plotting/showfig.rst.txt deleted file mode 100644 index 851aa246..00000000 --- a/doc_build/_build/html/_sources/utils/plotting/showfig.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_showfig: - -showfig (pyleoclim.utils.plotting.showfig) -================================= - -.. autofunction:: pyleoclim.utils.plotting.showfig diff --git a/doc_build/_build/html/_sources/utils/plotting/stackplot.rst.txt b/doc_build/_build/html/_sources/utils/plotting/stackplot.rst.txt deleted file mode 100644 index 538bfd63..00000000 --- a/doc_build/_build/html/_sources/utils/plotting/stackplot.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _plotting_stackplot: - -stackplot (pyleoclim.utils.plotting.stackplot) -============================================== - -.. autofunction:: pyleoclim.utils.plotting.stackplot diff --git a/doc_build/_build/html/_sources/utils/spectral/lombscargle.rst.txt b/doc_build/_build/html/_sources/utils/spectral/lombscargle.rst.txt deleted file mode 100644 index 0d1acd9c..00000000 --- a/doc_build/_build/html/_sources/utils/spectral/lombscargle.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_lombscargle: - -lomb_scargle (pyleoclim.utils.spectral.lomb_scargle) -===================================== - -.. autofunction:: pyleoclim.utils.spectral.lomb_scargle diff --git a/doc_build/_build/html/_sources/utils/spectral/mtm.rst.txt b/doc_build/_build/html/_sources/utils/spectral/mtm.rst.txt deleted file mode 100644 index e5789b46..00000000 --- a/doc_build/_build/html/_sources/utils/spectral/mtm.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_mtm: - -mtm (pyleoclim.utils.spectral.mtm) -===================================== - -.. autofunction:: pyleoclim.utils.spectral.mtm diff --git a/doc_build/_build/html/_sources/utils/spectral/periodogram.rst.txt b/doc_build/_build/html/_sources/utils/spectral/periodogram.rst.txt deleted file mode 100644 index 41800f10..00000000 --- a/doc_build/_build/html/_sources/utils/spectral/periodogram.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_periodogram: - -periodogram (pyleoclim.utils.spectral.periodogram) -===================================== - -.. autofunction:: pyleoclim.utils.spectral.periodogram diff --git a/doc_build/_build/html/_sources/utils/spectral/welch.rst.txt b/doc_build/_build/html/_sources/utils/spectral/welch.rst.txt deleted file mode 100644 index c75595dc..00000000 --- a/doc_build/_build/html/_sources/utils/spectral/welch.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_welch: - -welch (pyleoclim.utils.spectral.welch) -===================================== - -.. autofunction:: pyleoclim.utils.spectral.welch diff --git a/doc_build/_build/html/_sources/utils/spectral/wwz_psd.rst.txt b/doc_build/_build/html/_sources/utils/spectral/wwz_psd.rst.txt deleted file mode 100644 index 51c4f0f1..00000000 --- a/doc_build/_build/html/_sources/utils/spectral/wwz_psd.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_wwzpsd: - -wwz_psd (pyleoclim.utils.spectral.wwz_psd) -===================================== - -.. autofunction:: pyleoclim.utils.spectral.wwz_psd diff --git a/doc_build/_build/html/_sources/utils/tsbase/clean_ts.rst.txt b/doc_build/_build/html/_sources/utils/tsbase/clean_ts.rst.txt deleted file mode 100644 index 1335624b..00000000 --- a/doc_build/_build/html/_sources/utils/tsbase/clean_ts.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_clean_ts: - -clean_ts (pyleoclim.utils.tsbase.clean_ts) -=================================== - -.. autofunction:: pyleoclim.utils.tsbase.clean_ts diff --git a/doc_build/_build/html/_sources/utils/tsbase/dropna.rst.txt b/doc_build/_build/html/_sources/utils/tsbase/dropna.rst.txt deleted file mode 100644 index 245f053d..00000000 --- a/doc_build/_build/html/_sources/utils/tsbase/dropna.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_dropna: - -dropna (pyleoclim.utils.tsbase.dropna) -======================================= - -.. autofunction:: pyleoclim.utils.tsbase.dropna diff --git a/doc_build/_build/html/_sources/utils/tsbase/is_evenly_spaced.rst.txt b/doc_build/_build/html/_sources/utils/tsbase/is_evenly_spaced.rst.txt deleted file mode 100644 index 30be5d22..00000000 --- a/doc_build/_build/html/_sources/utils/tsbase/is_evenly_spaced.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_is_evenly_spaced: - -is_evenly_spaced (pyleoclim.utils.tsbase.is_evenly_spaced) -=================================================== - -.. autofunction:: pyleoclim.utils.tsbase.is_evenly_spaced diff --git a/doc_build/_build/html/_sources/utils/tsbase/reduce_duplicated_timestamp.rst.txt b/doc_build/_build/html/_sources/utils/tsbase/reduce_duplicated_timestamp.rst.txt deleted file mode 100644 index 0af38b3c..00000000 --- a/doc_build/_build/html/_sources/utils/tsbase/reduce_duplicated_timestamp.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_reduce_duplicated_timestamps: - -reduce_duplicated_timestamps (pyleoclim.utils.tsbase.reduce_duplicated_timestamps) -=================================================================================== - -.. autofunction:: pyleoclim.utils.tsbase.reduce_duplicated_timestamps diff --git a/doc_build/_build/html/_sources/utils/tsbase/sort_ts.rst.txt b/doc_build/_build/html/_sources/utils/tsbase/sort_ts.rst.txt deleted file mode 100644 index 1f58415e..00000000 --- a/doc_build/_build/html/_sources/utils/tsbase/sort_ts.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_sort_ts: - -sort_ts (pyleoclim.utils.tsbase.sort_tsa) -========================================== - -.. autofunction:: pyleoclim.utils.tsbase.sort_ts diff --git a/doc_build/_build/html/_sources/utils/tsmodel/ar1_fit.rst.txt b/doc_build/_build/html/_sources/utils/tsmodel/ar1_fit.rst.txt deleted file mode 100644 index 0c9b89ea..00000000 --- a/doc_build/_build/html/_sources/utils/tsmodel/ar1_fit.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _tsmodel_ar1_fit: - -ar1_fit (pyleoclim.utils.tsmodel.ar1_fit) -========================================= - -.. autofunction:: pyleoclim.utils.tsmodel.ar1_fit diff --git a/doc_build/_build/html/_sources/utils/tsmodel/ar1_fit_evenly.rst.txt b/doc_build/_build/html/_sources/utils/tsmodel/ar1_fit_evenly.rst.txt deleted file mode 100644 index 8bf32ec5..00000000 --- a/doc_build/_build/html/_sources/utils/tsmodel/ar1_fit_evenly.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _tsmodel_ar1_fit_evenly: - -ar1_fit_evenly (pyleoclim.utils.tsmodel.ar1_fit_evenly) -======================================================= - -.. autofunction:: pyleoclim.utils.tsmodel.ar1_fit_evenly diff --git a/doc_build/_build/html/_sources/utils/tsmodel/ar1_model.rst.txt b/doc_build/_build/html/_sources/utils/tsmodel/ar1_model.rst.txt deleted file mode 100644 index 33f87ddc..00000000 --- a/doc_build/_build/html/_sources/utils/tsmodel/ar1_model.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _tsmodel_ar1_model: - -ar1_model (pyleoclim.utils.tsmodel.ar1_model) -============================================= - -.. autofunction:: pyleoclim.utils.tsmodel.ar1_model diff --git a/doc_build/_build/html/_sources/utils/tsmodel/ar1_sim.rst.txt b/doc_build/_build/html/_sources/utils/tsmodel/ar1_sim.rst.txt deleted file mode 100644 index 5ab51198..00000000 --- a/doc_build/_build/html/_sources/utils/tsmodel/ar1_sim.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_ar1_sim: - -ar1_sim (pyleoclim.utils.tsmodel.ar1_sim) -================================= - -.. autofunction:: pyleoclim.utils.tsmodel.ar1_sim diff --git a/doc_build/_build/html/_sources/utils/tsmodel/colored_noise.rst.txt b/doc_build/_build/html/_sources/utils/tsmodel/colored_noise.rst.txt deleted file mode 100644 index 68978f4b..00000000 --- a/doc_build/_build/html/_sources/utils/tsmodel/colored_noise.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_colored_noise: - -colored_noise (pyleoclim.utils.tsmodel.colored_noise) -===================================================== - -.. autofunction:: pyleoclim.utils.tsmodel.colored_noise diff --git a/doc_build/_build/html/_sources/utils/tsmodel/colored_noise_2regimes.rst.txt b/doc_build/_build/html/_sources/utils/tsmodel/colored_noise_2regimes.rst.txt deleted file mode 100644 index 51ff5d3e..00000000 --- a/doc_build/_build/html/_sources/utils/tsmodel/colored_noise_2regimes.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_colored_noise_2regimes: - -colored_noise_2regimes (pyleoclim.utils.tsmodel.colored_noise_2regimes) -======================================================================= - -.. autofunction:: pyleoclim.utils.tsmodel.colored_noise_2regimes diff --git a/doc_build/_build/html/_sources/utils/tsmodel/gen_ar1_evenly.rst.txt b/doc_build/_build/html/_sources/utils/tsmodel/gen_ar1_evenly.rst.txt deleted file mode 100644 index 34b5430a..00000000 --- a/doc_build/_build/html/_sources/utils/tsmodel/gen_ar1_evenly.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_gen_ar1_evenly: - -gen_ar1_evenly (pyleoclim.utils.tsmodel.gen_ar1_evenly) -======================================================= - -.. autofunction:: pyleoclim.utils.tsmodel.gen_ar1_evenly diff --git a/doc_build/_build/html/_sources/utils/tsmodel/tau_estimation.rst.txt b/doc_build/_build/html/_sources/utils/tsmodel/tau_estimation.rst.txt deleted file mode 100644 index d9df0224..00000000 --- a/doc_build/_build/html/_sources/utils/tsmodel/tau_estimation.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _tsmodel_tau_estimation: - -tau_estimation (pyleoclim.utils.tsmodel.tau_estimation) -======================================================= - -.. autofunction:: pyleoclim.utils.tsmodel.tau_estimation diff --git a/doc_build/_build/html/_sources/utils/tsutils/annualize.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/annualize.rst.txt deleted file mode 100644 index d72f4e3a..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/annualize.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_annualize: - -annualize (pyleoclim.utils.tsutils.annualize) -===================================== - -.. autofunction:: pyleoclim.utils.tsutils.annualize diff --git a/doc_build/_build/html/_sources/utils/tsutils/bin_values.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/bin_values.rst.txt deleted file mode 100644 index ab22d64b..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/bin_values.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_bin: - -bin (pyleoclim.utils.tsutils.bin) -======================================= - -.. autofunction:: pyleoclim.utils.tsutils.bin diff --git a/doc_build/_build/html/_sources/utils/tsutils/detect_outliers.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/detect_outliers.rst.txt deleted file mode 100644 index 34b5542c..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/detect_outliers.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_detect_outliers: - -detect_outliers (pyleoclim.utils.tsutils.detect_outliers) -================================================= - -.. autofunction:: pyleoclim.utils.tsutils.detect_outliers diff --git a/doc_build/_build/html/_sources/utils/tsutils/detrend.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/detrend.rst.txt deleted file mode 100644 index 0247e37a..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/detrend.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_detrend: - -detrend (pyleoclim.utils.tsutils.detrend) -================================= - -.. autofunction:: pyleoclim.utils.tsutils.detrend diff --git a/doc_build/_build/html/_sources/utils/tsutils/distance_neighbors.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/distance_neighbors.rst.txt deleted file mode 100644 index 06da9ee0..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/distance_neighbors.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_tsutils_distance_neighbors: - -distance_neighbors (pyleoclim.utils.tsutils.distance_neighbors) -=============================================================== - -.. autofunction:: pyleoclim.utils.tsutils.distance_neighbors diff --git a/doc_build/_build/html/_sources/utils/tsutils/find_knee.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/find_knee.rst.txt deleted file mode 100644 index ee66a964..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/find_knee.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_tsutils_find_knee: - -find_knee (pyleoclim.utils.tsutils.find_knee) -============================================= - -.. autofunction:: pyleoclim.utils.tsutils.find_knee diff --git a/doc_build/_build/html/_sources/utils/tsutils/gaussianize.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/gaussianize.rst.txt deleted file mode 100644 index 533179b3..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/gaussianize.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_gaussianize: - -gaussianize (pyleoclim.utils.tsutils.gaussianize) -========================================= - -.. autofunction:: pyleoclim.utils.tsutils.gaussianize diff --git a/doc_build/_build/html/_sources/utils/tsutils/gaussianize_single.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/gaussianize_single.rst.txt deleted file mode 100644 index 5aec4f2f..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/gaussianize_single.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_gaussianize_single: - -gaussianize_single (pyleoclim.utils.tsutils.gaussianize_single) -======================================================= - -.. autofunction:: pyleoclim.utils.tsutils.gaussianize_single diff --git a/doc_build/_build/html/_sources/utils/tsutils/gkernel.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/gkernel.rst.txt deleted file mode 100644 index c2cc82e7..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/gkernel.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_gkernel: - -gkernel (pyleoclim.utils.tsutils.gkernel) -======================================= - -.. autofunction:: pyleoclim.utils.tsutils.gkernel diff --git a/doc_build/_build/html/_sources/utils/tsutils/grid_properties.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/grid_properties.rst.txt deleted file mode 100644 index d5032b99..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/grid_properties.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_grid_properties: - -grid_properties (pyleoclim.utils.tsutils.grid_properties) -======================================================== - -.. autofunction:: pyleoclim.utils.tsutils.grid_properties diff --git a/doc_build/_build/html/_sources/utils/tsutils/interp.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/interp.rst.txt deleted file mode 100644 index 786669bd..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/interp.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_interp: - -interp (pyleoclim.utils.tsutils.interp) -=============================== - -.. autofunction:: pyleoclim.utils.tsutils.interp diff --git a/doc_build/_build/html/_sources/utils/tsutils/on_common_axis.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/on_common_axis.rst.txt deleted file mode 100644 index 77dd20ce..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/on_common_axis.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_on_common_axis: - -on_common_axis (pyleoclim.utils.tsutils.on_common_axis) -=============================================== - -.. autofunction:: pyleoclim.utils.tsutils.on_common_axis diff --git a/doc_build/_build/html/_sources/utils/tsutils/preprocess.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/preprocess.rst.txt deleted file mode 100644 index 0b907a34..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/preprocess.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_tsutils_preprocess: - -preprocess (pyleoclim.utils.tsutils.preprocess) -=============================================== - -.. autofunction:: pyleoclim.utils.tsutils.preprocess diff --git a/doc_build/_build/html/_sources/utils/tsutils/remove_outliers.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/remove_outliers.rst.txt deleted file mode 100644 index 9047d755..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/remove_outliers.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_remove_outliers: - -remove_outliers (pyleoclim.utils.tsutils.remove_outliers) -================================================= - -.. autofunction:: pyleoclim.utils.tsutils.remove_outliers diff --git a/doc_build/_build/html/_sources/utils/tsutils/simple_stats.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/simple_stats.rst.txt deleted file mode 100644 index 81970c87..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/simple_stats.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_simple_stats: - -simple_stats (pyleoclim.utils.tsutils.simple_stats) -=========================================== - -.. autofunction:: pyleoclim.utils.tsutils.simple_stats diff --git a/doc_build/_build/html/_sources/utils/tsutils/standardize.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/standardize.rst.txt deleted file mode 100644 index 77f2e350..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/standardize.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_standardize: - -standardize (pyleoclim.utils.tsutils.standardize) -========================================= - -.. autofunction:: pyleoclim.utils.tsutils.standardize diff --git a/doc_build/_build/html/_sources/utils/tsutils/ts2segments.rst.txt b/doc_build/_build/html/_sources/utils/tsutils/ts2segments.rst.txt deleted file mode 100644 index cfd95cbb..00000000 --- a/doc_build/_build/html/_sources/utils/tsutils/ts2segments.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_ts2segments: - -ts2segments (pyleoclim.utils.tsutils.ts2segments) -========================================= - -.. autofunction:: pyleoclim.utils.tsutils.ts2segments diff --git a/doc_build/_build/html/_sources/utils/wavelet/AliasFilter.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/AliasFilter.rst.txt deleted file mode 100644 index 884679e8..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/AliasFilter.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_AliasFilter: - -AliasFilter (pyleoclim.utils.wavelet.AliasFilter) -================================================= - -.. autoclass:: pyleoclim.utils.wavelet.AliasFilter diff --git a/doc_build/_build/html/_sources/utils/wavelet/assertPositiveInt.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/assertPositiveInt.rst.txt deleted file mode 100644 index 34836d14..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/assertPositiveInt.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_assertPositiveInt: - -assertPositiveInt (pyleoclim.utils.wavelet.assertPositiveInt) -============================================================= - -.. autofunction:: pyleoclim.utils.wavelet.assertPositiveInt diff --git a/doc_build/_build/html/_sources/utils/wavelet/beta2HurstIndex.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/beta2HurstIndex.rst.txt deleted file mode 100644 index 87622bdb..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/beta2HurstIndex.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_beta2HurstIndex: - -beta2HurstIndex (pyleoclim.utils.wavelet.beta2HurstIndex) -========================================================= - -.. autofunction:: pyleoclim.utils.wavelet.beta2HurstIndex diff --git a/doc_build/_build/html/_sources/utils/wavelet/beta_estimation.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/beta_estimation.rst.txt deleted file mode 100644 index 9f289ddf..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/beta_estimation.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_beta_estimation: - -beta_estimation (pyleoclim.utils.wavelet.beta_estimation) -========================================================= - -.. autofunction:: pyleoclim.utils.wavelet.beta_estimation diff --git a/doc_build/_build/html/_sources/utils/wavelet/cross_wt.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/cross_wt.rst.txt deleted file mode 100644 index 053b5e22..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/cross_wt.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_cross_wt: - -cross_wt (pyleoclim.utils.wavelet.cross_wt) -=========================================== - -.. autofunction:: pyleoclim.utils.wavelet.cross_wt diff --git a/doc_build/_build/html/_sources/utils/wavelet/fBMsim.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/fBMsim.rst.txt deleted file mode 100644 index e0fc8b7b..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/fBMsim.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_fBMsim: - -fBMsim (pyleoclim.utils.wavelet.fBMsim) -======================================= - -.. autofunction:: pyleoclim.utils.wavelet.fBMsim diff --git a/doc_build/_build/html/_sources/utils/wavelet/freq_vector_log.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/freq_vector_log.rst.txt deleted file mode 100644 index 1b16cbf6..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/freq_vector_log.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_freq_vector_log: - -freq_vector_log (pyleoclim.utils.wavelet.freq_vector_log) -========================================================= - -.. autofunction:: pyleoclim.utils.wavelet.freq_vector_log diff --git a/doc_build/_build/html/_sources/utils/wavelet/freq_vector_lomb_scargle.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/freq_vector_lomb_scargle.rst.txt deleted file mode 100644 index 4e9cd3f9..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/freq_vector_lomb_scargle.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_freq_vector_lomb_scargle: - -freq_vector_lomb_scargle (pyleoclim.utils.wavelet.freq_vector_lomb_scargle) -=========================================================================== - -.. autofunction:: pyleoclim.utils.wavelet.freq_vector_lomb_scargle diff --git a/doc_build/_build/html/_sources/utils/wavelet/freq_vector_nfft.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/freq_vector_nfft.rst.txt deleted file mode 100644 index 8a9fcd5d..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/freq_vector_nfft.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_freq_vector_nfft: - -freq_vector_nfft (pyleoclim.utils.wavelet.freq_vector_nfft) -=========================================================== - -.. autofunction:: pyleoclim.utils.wavelet.freq_vector_nfft diff --git a/doc_build/_build/html/_sources/utils/wavelet/freq_vector_scale.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/freq_vector_scale.rst.txt deleted file mode 100644 index e1ca48fe..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/freq_vector_scale.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_freq_vector_scale: - -freq_vector_scale (pyleoclim.utils.wavelet.freq_vector_scale) -============================================================= - -.. autofunction:: pyleoclim.utils.wavelet.freq_vector_scale diff --git a/doc_build/_build/html/_sources/utils/wavelet/freq_vector_welch.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/freq_vector_welch.rst.txt deleted file mode 100644 index ed10b66a..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/freq_vector_welch.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_freq_vector_welch: - -freq_vector_welch (pyleoclim.utils.wavelet.freq_vector_welch) -============================================================= - -.. autofunction:: pyleoclim.utils.wavelet.freq_vector_welch diff --git a/doc_build/_build/html/_sources/utils/wavelet/get_wwz_func.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/get_wwz_func.rst.txt deleted file mode 100644 index d8830def..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/get_wwz_func.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_get_wwz_func: - -make_coi (pyleoclim.utils.wavelet.get_wwz_func) -=============================================== - -.. autofunction:: pyleoclim.utils.wavelet.get_wwz_func diff --git a/doc_build/_build/html/_sources/utils/wavelet/kirchner_basic.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/kirchner_basic.rst.txt deleted file mode 100644 index dcf84328..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/kirchner_basic.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_kirchner_basic: - -kirchner_basic (pyleoclim.utils.wavelet.kirchner_basic) -======================================================= - -.. autofunction:: pyleoclim.utils.wavelet.kirchner_basic diff --git a/doc_build/_build/html/_sources/utils/wavelet/kirchner_f2py.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/kirchner_f2py.rst.txt deleted file mode 100644 index 68908c22..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/kirchner_f2py.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_kirchner_f2py: - -kirchner_f2py (pyleoclim.utils.wavelet.kirchner_f2py) -======================================================= - -.. autofunction:: pyleoclim.utils.wavelet.kirchner_f2py diff --git a/doc_build/_build/html/_sources/utils/wavelet/kirchner_nproc.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/kirchner_nproc.rst.txt deleted file mode 100644 index 518a7d83..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/kirchner_nproc.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_kirchner_nproc: - -kirchner_nproc (pyleoclim.utils.wavelet.kirchner_nproc) -======================================================= - -.. autofunction:: pyleoclim.utils.wavelet.kirchner_nproc diff --git a/doc_build/_build/html/_sources/utils/wavelet/kirchner_numba.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/kirchner_numba.rst.txt deleted file mode 100644 index 7f3a8782..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/kirchner_numba.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_kirchner_numba: - -kirchner_numba (pyleoclim.utils.wavelet.kirchner_numba) -======================================================= - -.. autofunction:: pyleoclim.utils.wavelet.kirchner_numba diff --git a/doc_build/_build/html/_sources/utils/wavelet/make_coi.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/make_coi.rst.txt deleted file mode 100644 index 451aaa75..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/make_coi.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_make_coi: - -make_coi (pyleoclim.utils.wavelet.make_coi) -=========================================== - -.. autofunction:: pyleoclim.utils.wavelet.make_coi diff --git a/doc_build/_build/html/_sources/utils/wavelet/make_freq_vector.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/make_freq_vector.rst.txt deleted file mode 100644 index 3a73c879..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/make_freq_vector.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_make_freq_vector: - -make_freq_vector (pyleoclim.utils.wavelet.make_freq_vector) -=========================================================== - -.. autofunction:: pyleoclim.utils.wavelet.make_freq_vector diff --git a/doc_build/_build/html/_sources/utils/wavelet/make_omega.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/make_omega.rst.txt deleted file mode 100644 index 233407ad..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/make_omega.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_make_omega: - -make_omega (pyleoclim.utils.wavelet.make_omega) -=========================================== - -.. autofunction:: pyleoclim.utils.wavelet.make_omega diff --git a/doc_build/_build/html/_sources/utils/wavelet/prepare_wwz.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/prepare_wwz.rst.txt deleted file mode 100644 index d418b112..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/prepare_wwz.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_prepare_wwz: - -prepare_wwz (pyleoclim.utils.wavelet.prepare_wwz) -================================================= - -.. autofunction:: pyleoclim.utils.wavelet.prepare_wwz diff --git a/doc_build/_build/html/_sources/utils/wavelet/private.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/private.rst.txt deleted file mode 100644 index 99270814..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/private.rst.txt +++ /dev/null @@ -1,92 +0,0 @@ -.. _wavelet_private: - -.. toctree:: - :hidden: - AliasFilter.rst - assertPositiveInt.rst - wwz_basic.rst - wwz_nproc.rst - kirchner_basic.rst - kirchner_nproc.rst - kirchner_numba.rst - kirchner_f2py.rst - make_coi.rst - make_omega.rst - wwa2psd.rst - freq_vector_lomb_scargle.rst - freq_vector_welch.rst - freq_vector_nfft.rst - freq_vector_scale.rst - freq_vector_log.rst - make_freq_vector.rst - beta_estimation.rst - beta2HurstIndex.rst - psd_ar.rst - fBMsim.rst - psd_fBm.rst - get_wwz_func.rst - prepare_wwz.rst - cross_wt.rst - wavelet_coherence.rst - reconstruct_ts.rst - -Wavelet and spectral preprocessing functions (pyleoclim.utils.wavelet) -====================================================================== -.. list-table:: - :widths: 30 70 - :header-rows: 0 - - * - :ref:`AliasFilter ` - - Performs anti-alis filter on a PSD. Experimental - * - :ref:`assertPositiveInt ` - - Asserts that the arguments are all positive integers - * - :ref:`wwz_basic ` - - Returns the weighted wavelet amplitude estimated from the original Foster method. No multiprocessing - * - :ref:`wwz_nproc ` - - Returns the weighted wavelet amplitude using the original method from Kirchner. Supports multiprocessing - * - :ref:`kirchner_basic ` - - Return the weighted wavelet amplitude (WWA) modified by Kirchner. No multiprocessing - * - :ref:`kirchner_nproc ` - - Returns the weighted wavelet amplitude (WWA) modified by Kirchner. Supports multiprocessing - * - :ref:`kirchner_numba ` - - Return the weighted wavelet amplitude (WWA) modified by Kirchner using Numba package. - * - :ref:`kirchner_f2py ` - - Returns the weighted wavelet amplitude (WWA) modified by Kirchner. Uses Fortran. Fastest method but requires a compiler. - * - :ref:`make_coi ` - - Return the cone of influence. - * - :ref:`make_omega ` - - Return the angular frequency based on the time axis and given frequency vector - * - :ref:`wwa2psd ` - - Return the power spectral density (PSD) using the weighted wavelet amplitude (WWA). - * - :ref:`freq_vector_lomb_scargle ` - - Return the frequency vector based on the REDFIT recommendation. - * - :ref:`freq_vector_welch ` - - Return the frequency vector based on the Welch's method. - * - :ref:`freq_vector_nfft ` - - Return the frequency vector based on NFFT - * - :ref:`freq_vector_scale ` - - Return the frequency vector based on scales - * - :ref:`freq_vector_log ` - - Return the frequency vector based on logspace - * - :ref:`make_freq_vector ` - - Make frequency vector - * - :ref:`beta_estimation ` - - Estimate the power slope of a 1/f^beta process. - * - :ref:`beta2HurstIndex ` - - Translate psd slope to Hurst index - * - :ref:`psd_ar ` - - Return the theoretical power spectral density (PSD) of an autoregressive model - * - :ref:`fBMsim ` - - Select an ensemble table from a list - * - :ref:`psd_fBM ` - - Return the theoretical psd of a fBM - * - :ref:`get_wwz_func ` - - Return the wwz function to use. - * - :ref:`prepare_wwz ` - - Return the truncated time series with NaNs deleted and estimate frequency vector and tau - * - :ref:`cross_wt ` - - Return the cross wavelet transform. - * - :ref:`wavelet_coherence ` - - Return the cross wavelet coherence. - * - :ref:`reconstruct_ts ` - - Reconstruct the normalized time series from the wavelet coefficients. diff --git a/doc_build/_build/html/_sources/utils/wavelet/psd_ar.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/psd_ar.rst.txt deleted file mode 100644 index b8605a71..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/psd_ar.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_psd_ar: - -psd_ar (pyleoclim.utils.wavelet.psd_ar) -======================================= - -.. autofunction:: pyleoclim.utils.wavelet.psd_ar diff --git a/doc_build/_build/html/_sources/utils/wavelet/psd_fBm.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/psd_fBm.rst.txt deleted file mode 100644 index 7d737f2f..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/psd_fBm.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_psd_fBM: - -psd_fBM (pyleoclim.utils.wavelet.psd_fBM) -========================================= - -.. autofunction:: pyleoclim.utils.wavelet.psd_fBM diff --git a/doc_build/_build/html/_sources/utils/wavelet/reconstruct_ts.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/reconstruct_ts.rst.txt deleted file mode 100644 index eecfc8f0..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/reconstruct_ts.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_reconstruct_ts: - -reconstruct_ts (pyleoclim.utils.wavelet.reconstruct_ts) -======================================================= - -.. autofunction:: pyleoclim.utils.wavelet.reconstruct_ts diff --git a/doc_build/_build/html/_sources/utils/wavelet/wavelet_coherence.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/wavelet_coherence.rst.txt deleted file mode 100644 index e0e79ba0..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/wavelet_coherence.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_wavelet_coherence: - -wavelet_coherence (pyleoclim.utils.wavelet.wavelet_coherence) -============================================================= - -.. autofunction:: pyleoclim.utils.wavelet.wavelet_coherence diff --git a/doc_build/_build/html/_sources/utils/wavelet/wwa2psd.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/wwa2psd.rst.txt deleted file mode 100644 index 87bb7dfe..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/wwa2psd.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_wwa2psd: - -wwa2psd (pyleoclim.utils.wavelet.wwa2psd) -========================================= - -.. autofunction:: pyleoclim.utils.wavelet.wwa2psd diff --git a/doc_build/_build/html/_sources/utils/wavelet/wwz.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/wwz.rst.txt deleted file mode 100644 index b156567f..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/wwz.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_wwz: - -wwz (pyleoclim.utils.wavelet.wwz) -========================= - -.. autofunction:: pyleoclim.utils.wavelet.wwz diff --git a/doc_build/_build/html/_sources/utils/wavelet/wwz_basic.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/wwz_basic.rst.txt deleted file mode 100644 index 59452fd8..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/wwz_basic.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_wwz_basic: - -wwz_basic (pyleoclim.utils.wavelet.wwz_basic) -============================================= - -.. autofunction:: pyleoclim.utils.wavelet.wwz_basic diff --git a/doc_build/_build/html/_sources/utils/wavelet/wwz_nproc.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/wwz_nproc.rst.txt deleted file mode 100644 index 62f126b3..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/wwz_nproc.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _wavelet_wwz_nproc: - -wwz_nproc (pyleoclim.utils.wavelet.wwz_nproc) -============================================= - -.. autofunction:: pyleoclim.utils.wavelet.wwz_nproc diff --git a/doc_build/_build/html/_sources/utils/wavelet/xwc.rst.txt b/doc_build/_build/html/_sources/utils/wavelet/xwc.rst.txt deleted file mode 100644 index 8467bef8..00000000 --- a/doc_build/_build/html/_sources/utils/wavelet/xwc.rst.txt +++ /dev/null @@ -1,6 +0,0 @@ -.. _utils_xwc: - -xwc (pyleoclim.utils.wavelet.xwc) -========================= - -.. autofunction:: pyleoclim.utils.wavelet.xwc diff --git a/doc_build/_build/html/_static/basic.css b/doc_build/_build/html/_static/basic.css deleted file mode 100644 index 912859b5..00000000 --- a/doc_build/_build/html/_static/basic.css +++ /dev/null @@ -1,904 +0,0 @@ -/* - * basic.css - * ~~~~~~~~~ - * - * Sphinx stylesheet -- basic theme. - * - * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * - */ - -/* -- main layout ----------------------------------------------------------- */ - -div.clearer { - clear: both; -} - -div.section::after { - display: block; - content: ''; - clear: left; -} - -/* -- relbar ---------------------------------------------------------------- */ - -div.related { - width: 100%; - font-size: 90%; -} - -div.related h3 { - display: none; -} - -div.related ul { - margin: 0; - padding: 0 0 0 10px; - list-style: none; -} - -div.related li { - display: inline; -} - -div.related li.right { - float: right; - margin-right: 5px; -} - -/* -- sidebar --------------------------------------------------------------- */ - -div.sphinxsidebarwrapper { - padding: 10px 5px 0 10px; -} - -div.sphinxsidebar { - float: left; - width: 230px; - margin-left: -100%; - font-size: 90%; - word-wrap: break-word; - overflow-wrap : break-word; -} - -div.sphinxsidebar ul { - list-style: none; -} - -div.sphinxsidebar ul ul, -div.sphinxsidebar ul.want-points { - margin-left: 20px; - list-style: square; -} - -div.sphinxsidebar ul ul { - margin-top: 0; - margin-bottom: 0; -} - -div.sphinxsidebar form { - margin-top: 10px; -} - -div.sphinxsidebar input { - border: 1px solid #98dbcc; - font-family: sans-serif; - font-size: 1em; -} - -div.sphinxsidebar #searchbox form.search { - overflow: hidden; -} - -div.sphinxsidebar #searchbox input[type="text"] { - float: left; - width: 80%; - padding: 0.25em; - box-sizing: border-box; -} - -div.sphinxsidebar #searchbox input[type="submit"] { - float: left; - width: 20%; - border-left: none; - padding: 0.25em; - box-sizing: border-box; -} - - -img { - border: 0; - max-width: 100%; -} - -/* -- search page ----------------------------------------------------------- */ - -ul.search { - margin: 10px 0 0 20px; - padding: 0; -} - -ul.search li { - padding: 5px 0 5px 20px; - background-image: url(file.png); - background-repeat: no-repeat; - background-position: 0 7px; -} - -ul.search li a { - font-weight: bold; -} - -ul.search li p.context { - color: #888; - margin: 2px 0 0 30px; - text-align: left; -} - -ul.keywordmatches li.goodmatch a { - font-weight: bold; -} - -/* -- index page ------------------------------------------------------------ */ - -table.contentstable { - width: 90%; - margin-left: auto; - margin-right: auto; -} - -table.contentstable p.biglink { - line-height: 150%; -} - -a.biglink { - font-size: 1.3em; -} - -span.linkdescr { - font-style: italic; - padding-top: 5px; - font-size: 90%; -} - -/* -- general index --------------------------------------------------------- */ - -table.indextable { - width: 100%; -} - -table.indextable td { - text-align: left; - vertical-align: top; -} - -table.indextable ul { - margin-top: 0; - margin-bottom: 0; - list-style-type: none; -} - -table.indextable > tbody > tr > td > ul { - padding-left: 0em; -} - -table.indextable tr.pcap { - height: 10px; -} - -table.indextable tr.cap { - margin-top: 10px; - background-color: #f2f2f2; -} - -img.toggler { - margin-right: 3px; - margin-top: 3px; - cursor: pointer; -} - -div.modindex-jumpbox { - border-top: 1px solid #ddd; - border-bottom: 1px solid #ddd; - margin: 1em 0 1em 0; - padding: 0.4em; -} - -div.genindex-jumpbox { - border-top: 1px solid #ddd; - border-bottom: 1px solid #ddd; - margin: 1em 0 1em 0; - padding: 0.4em; -} - -/* -- domain module index --------------------------------------------------- */ - -table.modindextable td { - padding: 2px; - border-collapse: collapse; -} - -/* -- general body styles --------------------------------------------------- */ - -div.body { - min-width: 450px; - max-width: 800px; -} - -div.body p, div.body dd, div.body li, div.body blockquote { - -moz-hyphens: auto; - -ms-hyphens: auto; - -webkit-hyphens: auto; - hyphens: auto; -} - -a.headerlink { - visibility: 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+13,6 @@ from .utils import * from .core import * -from .utils import plotting -plotting.set_style() - # get the version from importlib.metadata import version __version__ = version('pyleoclim') diff --git a/pyleoclim/utils/plotting.py b/pyleoclim/utils/plotting.py index 2234419b..ee7b4001 100644 --- a/pyleoclim/utils/plotting.py +++ b/pyleoclim/utils/plotting.py @@ -372,17 +372,19 @@ def showfig(fig, close=False): pyleoclim.utils.plotting.in_notebook: Functions to sense a notebook environment ''' - if in_notebook: - try: - from IPython.display import display - except ImportError as error: - # Output expected ImportErrors. - print(f'{error.__class__.__name__}: {error.message}') + # if in_notebook: + # try: + # from IPython.display import display + # except ImportError as error: + # # Output expected ImportErrors. + # print(f'{error.__class__.__name__}: {error.message}') - display(fig) + # display(fig) - else: - plt.show() + # else: + # plt.show() + + plt.show() if close: closefig(fig)