diff --git a/docs/contributing.rst b/docs/contributing.rst index 6948bc833..b0e2bd83a 100644 --- a/docs/contributing.rst +++ b/docs/contributing.rst @@ -24,21 +24,21 @@ This will let you run the program with the latest modification, without requirin If you want to check, type ``python --version`` in a terminal. -Linux, Mac and Windows developer installation ------------------------------------- +Linux, Mac and Windows developer installation +--------------------------------------------- Be sure to have ``git`` and ``pip`` installed. Fork the phys2bids repository in GitHub, then open a terminal and run the following code to clone the forked repository and set it as your `origin`:: - git clone https://github.com/{username}/phys2bids.git - # or in case you have an ssh key set up: - git clone git@github.com:{username}/phys2bids.git + git clone https://github.com/{username}/phys2bids.git + # or in case you prefer to use ssh: + git clone git@github.com:{username}/phys2bids.git We also recommend to set up the physiopy/phys2bids repository as `upstream`. In this way you can always keep your main branch up to date with the command `git pull upstream master`:: - cd phys2bids - git remote add upstream https://github.com/physiopy/phys2bids.git - git pull upstream master + cd phys2bids + git remote add upstream https://github.com/physiopy/phys2bids.git + git pull upstream master Basic installation @@ -49,7 +49,7 @@ are already installed in your system. Move into the ``phys2bids`` folder and execute the command:: - pip3 install -e . + pip3 install -e . Full developer installation ^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -59,48 +59,47 @@ to collaborate with us, you can install ``phys2bids`` with all the other package Move into the ``phys2bids`` folder and execute the command:: - pip3 install -e .[all] + pip3 install -e .[all] This will install: - - ``phys2bids`` as an editable package, which means that you can modify the program and run it without having to reinstall it every time! - - All the ``phys2bids`` dependencies. - - All the **interface** modules, that deal with the interfaces for all the file formats. - - All the **style** modules, such as ``flake8``, to help you linter the code! - - All the **documentation** modules, like ``sphinx``, so that you can build the docs locally before submitting them. - - All the **test** modules, like ``pytest``, in order for you to test your code locally before committing it! + - ``phys2bids`` as an editable package, which means that you can modify the program and run it without having to reinstall it every time! + - All the ``phys2bids`` dependencies. + - All the **interface** modules, that deal with the interfaces for all the file formats. + - All the **style** modules, such as ``flake8``, to help you linter the code! + - All the **documentation** modules, like ``sphinx``, so that you can build the docs locally before submitting them. + - All the **test** modules, like ``pytest``, in order for you to test your code locally before committing it! Check your installation! ^^^^^^^^^^^^^^^^^^^^^^^^ Type the commands:: - cd phys2bids/tests + cd phys2bids/tests pytest This will execute the tests locally and check that your phys2bids installation works properly. .. code-block:: shell - pytest - =================================================================== test session starts =================================================================== - platform win32 -- Python 3.8.6, pytest-6.1.1, py-1.9.0, pluggy-0.13.1 - rootdir: C:\Users\sento\phys2bids, configfile: setup.cfg - plugins: cov-2.10.1 - collected 61 items - - test_acq.py . [ 1%] - test_bids.py ................ [ 27%] - test_integration.py ... [ 32%] - test_phys2bids.py ... [ 37%] - test_physio_obj.py ....... [ 49%] - test_txt.py .................. [ 78%] - test_utils.py ........... [ 96%] - test_viz.py .x [100%] - - ================================================================= short test summary info ================================================================= - XFAIL test_viz.py::test_plot_trigger - ======================================================== 60 passed, 1 xfailed in 142.58s (0:02:22) ======================================================== - -Do Not worry about the xfail error in the test_viz.py, this is only happening because at the moment we cannot run this test in our Continous integration workflow. -However if you do encounter any other error, check that you have all the extra dependencies install and contact us if necessary. \ No newline at end of file + pytest + =================================== test session starts =================================== + platform win32 -- Python 3.8.6, pytest-6.1.1, py-1.9.0, pluggy-0.13.1 + rootdir: C:\Users\sento\phys2bids, configfile: setup.cfg + plugins: cov-2.10.1 + collected 61 items + + test_acq.py . [ 1%] + test_bids.py ................ [ 27%] + test_integration.py ... [ 32%] + test_phys2bids.py ... [ 37%] + test_physio_obj.py ....... [ 49%] + test_txt.py .................. [ 78%] + test_utils.py ........... [ 96%] + test_viz.py .x [100%] + + ================================= short test summary info ================================= + XFAIL test_viz.py::test_plot_trigger + ======================== 60 passed, 1 xfailed in 142.58s (0:02:22) ======================== + +Do **not** worry if there is a xfail error in the log. This happens when we know that a test will fail for known reasons, and we are probably working to fix it (see `here `_. However, if you do encounter any other error, check that you have all the extra dependencies installed and their version meets ``phys2bids`` requirements. Contact us on `gitter `_ if you need help! \ No newline at end of file diff --git a/docs/installation.rst b/docs/installation.rst index d4561ad50..7a7278442 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -35,39 +35,30 @@ Install with ``pip`` Install ``phys2bids`` alone ~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Pypi has the latest stable release of ``phys2bids`` as a package. Just run:: +Pypi has the latest stable release of ``phys2bids`` as a package. Since we use ``auto`` to publish the latest features as soon as they are ready, it will *really* be the latest release. Just run:: pip3 install phys2bids -If you want the latest development version of the program, download the package from `github `_ and uncompress it. -Alternatively, if you have ``git``, use the command:: - - git clone https://github.com/physiopy/phys2bids.git - -Open a terminal in the ``phys2bids`` folder and execute the command:: - - pip3 install . - Install extra modules ~~~~~~~~~~~~~~~~~~~~~ If you are planning to use file formats other than plain ``txt``, you need to install extra modules to have the right interface. Extra modules installation can be done with the syntax:: - pip3 install [] + pip3 install phys2bids[] -Where ``>`` is either ``phys2bids`` or ``.``, depending on whether you want to use ``pip`` or ``git`` for the installation, and ```` is one of the following: +Where ```` is one of the following: - ``acq``: if you plan to use native AcqKnowledge files (``.acq`` extension) - ``interfaces``: for all the interfaces above. -For instance, if you plan to install ``phys2bids`` and use all the interfaces, run:: +For instance, if you plan to install ``phys2bids`` and use all of the interfaces, run:: pip3 install phys2bids[interfaces] .. note:: If you "missed" or skipped this trick when you installed ``phys2bids`` the first time, don't worry! - You can do it any time - this will update ``phys2bids`` and install all the extra modules you want. + You can do it any time - this will update ``phys2bids`` and install all extra modules you want. Install without ``pip`` @@ -94,39 +85,25 @@ Type the command:: phys2bids -v -If your output is: ``phys2bids 1.3.0-beta`` or similar, ``phys2bids`` is ready to be used. +If your output is: ``phys2bids 2.2.2`` or similar, ``phys2bids`` is ready to be used. Windows installation --------------------------- +-------------------- -First of all let's check you have python installed. Open a windows power shell window in ADMIN MODE and type:: +First of all let's check you have python installed. Open a windows power shell window in **admin mode** and type:: python --version -In case you don't have it, either install it from this link https://www.microsoft.com/en-us/p/python-38/9mssztt1n39l?activetab=pivot:overviewtab or type the command:: +In case you don't have it, either install it from `here `_ or type the command:: python It will redirect you to the windows store python install (in the creation of this tutorial the newest version of python was 3.8). -Once python is installed, you can either install phys2bids directly with pip:: - - pip install phys2bids +.. warning:: + ``phys2bids`` supports Python 3.6 and later versions. We can't guarantee it will work if you use python 2. -If you want the latest development version of the program, download the package from `github `_ and uncompress it. -Alternatively, if you have ``git``, use the command:: - - git clone https://github.com/physiopy/phys2bids.git +Once python is installed, you can follow the instructions to install ``phys2bids`` reported `above <#install-with-pip>`_ -Open a terminal in the ``phys2bids`` folder in ADMIN MODE and execute the command:: - - pip install . - # or if you want all the extra dependencies installed: - pip install .[all] - -Check your installation! -^^^^^^^^^^^^^^^^^^^^^^^^ - -Type the command:: - - phys2bids -v +.. note:: + Remember to open a terminal in **admin mode** to install libraries!