From cab7c7ab9692c77a706310b34cde5ab2d9b45a44 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Wed, 15 Jan 2025 10:42:51 +0000 Subject: [PATCH 1/7] Added mention of the fact that getting started instructions need to be run in terminal --- docs/source/using_the_ve/getting_started.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/source/using_the_ve/getting_started.md b/docs/source/using_the_ve/getting_started.md index 2dc39db24..cb09ebf2c 100644 --- a/docs/source/using_the_ve/getting_started.md +++ b/docs/source/using_the_ve/getting_started.md @@ -28,8 +28,9 @@ language_info: ## Installing the Virtual Ecosystem model For most users the best way to get started with the Virtual Ecosystem package is to -[install Python](https://www.python.org/downloads/) and then install the Virtual -Ecosystem using the `pip` package installer. +first [install Python](https://www.python.org/downloads/). Then open a terminal window +and use the following command to install the Virtual Ecosystem using the `pip` package +installer. ```sh pip install virtual-ecosystem @@ -41,7 +42,7 @@ that the package is still being developed so these are currently early developme If you are more interested in playing around with the development of the model, then you will need to follow the [overview of the code contribution -process]../development/contributing/overivew.md), which covers the installation of the +process](../development/contributing/overivew.md), which covers the installation of the tools required for code development, testing and building documentation. ## Running an example Virtual Ecosystem simulation From 94d04cbfb1e28ff0c24b5d60e9dac42a168dd103 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Wed, 15 Jan 2025 11:33:41 +0000 Subject: [PATCH 2/7] Added seperate windows and unix tabs for the example installation step --- docs/source/conf.py | 1 + docs/source/using_the_ve/getting_started.md | 16 ++++++++++---- poetry.lock | 24 +++++++++++++++++++-- pyproject.toml | 1 + 4 files changed, 36 insertions(+), 6 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 631adfda9..56adb9b98 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -101,6 +101,7 @@ "sphinx_external_toc", "sphinx_design", "hoverxref.extension", + "sphinx_tabs.tabs", ] autodoc_default_flags = ["members"] autosummary_generate = True diff --git a/docs/source/using_the_ve/getting_started.md b/docs/source/using_the_ve/getting_started.md index cb09ebf2c..beb428e3b 100644 --- a/docs/source/using_the_ve/getting_started.md +++ b/docs/source/using_the_ve/getting_started.md @@ -42,7 +42,7 @@ that the package is still being developed so these are currently early developme If you are more interested in playing around with the development of the model, then you will need to follow the [overview of the code contribution -process](../development/contributing/overivew.md), which covers the installation of the +process](../development/contributing/overview.md), which covers the installation of the tools required for code development, testing and building documentation. ## Running an example Virtual Ecosystem simulation @@ -53,15 +53,23 @@ first need to install the data to a location of your choice. The command below w create the `ve_example` directory at the location you choose and install all of the configuration and data files to run a model. -```shell -ve_run --install-example /path/ +````{tabs} +```{group-tab} macOS/Linux + ```shell + ve_run --install-example /path/ ``` +```{group-tab} Windows + ```powershell + ve_run --install-example \path\ + +```` + You can then run the model itself: ```shell ve_run /path/ve_example/config \ - --outpath /path/ve_example/config/out \ + --outpath /path/ve_example/out \ --logfile /path/ve_example/out/ve_example.log ``` diff --git a/poetry.lock b/poetry.lock index 1a26b08f4..2e75fff88 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "alabaster" @@ -4025,6 +4025,26 @@ sphinxcontrib-jquery = ">=4,<5" [package.extras] dev = ["bump2version", "transifex-client", "twine", "wheel"] +[[package]] +name = "sphinx-tabs" +version = "3.4.7" +description = "Tabbed views for Sphinx" +optional = false +python-versions = ">=3.7" +files = [ + {file = "sphinx-tabs-3.4.7.tar.gz", hash = "sha256:991ad4a424ff54119799ba1491701aa8130dd43509474aef45a81c42d889784d"}, + {file = "sphinx_tabs-3.4.7-py3-none-any.whl", hash = "sha256:c12d7a36fd413b369e9e9967a0a4015781b71a9c393575419834f19204bd1915"}, +] + +[package.dependencies] +docutils = "*" +pygments = "*" +sphinx = ">=1.8" + +[package.extras] +code-style = ["pre-commit (==2.13.0)"] +testing = ["bs4", "coverage", "pygments", "pytest (>=7.1,<8)", "pytest-cov", "pytest-regressions", "rinohtype"] + [[package]] name = "sphinxcontrib-applehelp" version = "2.0.0" @@ -4735,4 +4755,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.13" -content-hash = "9a4ec2b0a7509c70a540b2aa317423ef706ff1bcd3b90c9a40b82b95a2df364d" +content-hash = "bfa10cbdfe2b709a15bbdf3d04fdbc0793b2f7a0b9bef228ffae73956287e3c9" diff --git a/pyproject.toml b/pyproject.toml index 12b0f52b5..ab31e9686 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -83,6 +83,7 @@ sphinx-rtd-theme = ">=2,<4" sphinxcontrib-bibtex = "^2.6.1" sphinxcontrib-mermaid = ">=0.9.2,<1.1.0" sphinx-hoverxref = "^1.4.1" +sphinx-tabs = "^3.4.7" [build-system] build-backend = "poetry.core.masonry.api" From fa12c2eefcb1c76fe7dada3f3a82e88e432b305c Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Wed, 15 Jan 2025 11:42:54 +0000 Subject: [PATCH 3/7] Added windows specific commands to run example simulation --- docs/source/using_the_ve/getting_started.md | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/docs/source/using_the_ve/getting_started.md b/docs/source/using_the_ve/getting_started.md index beb428e3b..f4dcd89a5 100644 --- a/docs/source/using_the_ve/getting_started.md +++ b/docs/source/using_the_ve/getting_started.md @@ -67,12 +67,22 @@ configuration and data files to run a model. You can then run the model itself: -```shell -ve_run /path/ve_example/config \ +````{tabs} +```{group-tab} macOS/Linux + ```shell + ve_run /path/ve_example/config \ --outpath /path/ve_example/out \ --logfile /path/ve_example/out/ve_example.log ``` +```{group-tab} Windows + ```powershell + ve_run \path\ve_example\config ` + --outpath \path\ve_example/out ` + --logfile \path\ve_example\out\ve_example.log +``` +```` + The [Virtual Ecosystem in use](virtual_ecosystem_in_use.md) page provides a walkthrough of this process, showing the typical outputs of the model run process, and also provides some simple plots of model inputs and ouputs. From 7c6d6f970d36815f333b1ce2b11f9d26f1edc284 Mon Sep 17 00:00:00 2001 From: Jacob Cook Date: Wed, 15 Jan 2025 13:41:02 +0000 Subject: [PATCH 4/7] Added C: in front of windows paths to make what they are meant to be more obvious --- docs/source/using_the_ve/getting_started.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/using_the_ve/getting_started.md b/docs/source/using_the_ve/getting_started.md index f4dcd89a5..c9b232fd4 100644 --- a/docs/source/using_the_ve/getting_started.md +++ b/docs/source/using_the_ve/getting_started.md @@ -61,7 +61,7 @@ configuration and data files to run a model. ```{group-tab} Windows ```powershell - ve_run --install-example \path\ + ve_run --install-example C:\path\ ```` @@ -77,9 +77,9 @@ You can then run the model itself: ```{group-tab} Windows ```powershell - ve_run \path\ve_example\config ` - --outpath \path\ve_example/out ` - --logfile \path\ve_example\out\ve_example.log + ve_run C:\path\ve_example\config ` + --outpath C:\path\ve_example/out ` + --logfile C:\path\ve_example\out\ve_example.log ``` ```` From db608b61fe40ce8c0797ddd21496b9b24b5458d4 Mon Sep 17 00:00:00 2001 From: Sally Date: Thu, 16 Jan 2025 11:21:28 +0000 Subject: [PATCH 5/7] Add specificaiton of python version and reccomend pyenv --- docs/source/using_the_ve/getting_started.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/docs/source/using_the_ve/getting_started.md b/docs/source/using_the_ve/getting_started.md index c9b232fd4..de3e30e77 100644 --- a/docs/source/using_the_ve/getting_started.md +++ b/docs/source/using_the_ve/getting_started.md @@ -28,9 +28,12 @@ language_info: ## Installing the Virtual Ecosystem model For most users the best way to get started with the Virtual Ecosystem package is to -first [install Python](https://www.python.org/downloads/). Then open a terminal window -and use the following command to install the Virtual Ecosystem using the `pip` package -installer. +first [install Python](https://www.python.org/downloads/). To use the Virtual Ecosystem +you will need Python 3.10, 3.11, or 3.12. If you are new to Python, we recommend using +`pyenv` or `pyenv-win` to install and manage versions of Python. + +Afer installing Python, open a terminal window and use the following command to install +the Virtual Ecosystem using the `pip` package installer. ```sh pip install virtual-ecosystem From 70d0c804a1aff10a7aafa68cc7251ec5f5f22927 Mon Sep 17 00:00:00 2001 From: Sally Matson Date: Thu, 16 Jan 2025 12:52:13 +0000 Subject: [PATCH 6/7] Update getting_started.md Removed reference to pyenv --- docs/source/using_the_ve/getting_started.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/source/using_the_ve/getting_started.md b/docs/source/using_the_ve/getting_started.md index de3e30e77..6e573a258 100644 --- a/docs/source/using_the_ve/getting_started.md +++ b/docs/source/using_the_ve/getting_started.md @@ -29,8 +29,7 @@ language_info: For most users the best way to get started with the Virtual Ecosystem package is to first [install Python](https://www.python.org/downloads/). To use the Virtual Ecosystem -you will need Python 3.10, 3.11, or 3.12. If you are new to Python, we recommend using -`pyenv` or `pyenv-win` to install and manage versions of Python. +you will need Python 3.10, 3.11, or 3.12. Afer installing Python, open a terminal window and use the following command to install the Virtual Ecosystem using the `pip` package installer. From c2ddebe81f82deddfcf23337a9d07767805f0afa Mon Sep 17 00:00:00 2001 From: Sally Matson Date: Tue, 21 Jan 2025 10:20:53 +0000 Subject: [PATCH 7/7] Fixed a slash --- docs/source/using_the_ve/getting_started.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/using_the_ve/getting_started.md b/docs/source/using_the_ve/getting_started.md index 6e573a258..d4d655327 100644 --- a/docs/source/using_the_ve/getting_started.md +++ b/docs/source/using_the_ve/getting_started.md @@ -80,7 +80,7 @@ You can then run the model itself: ```{group-tab} Windows ```powershell ve_run C:\path\ve_example\config ` - --outpath C:\path\ve_example/out ` + --outpath C:\path\ve_example\out ` --logfile C:\path\ve_example\out\ve_example.log ``` ````