From 49b31a5fdd110b744a433d29a9b71fbc756048db Mon Sep 17 00:00:00 2001 From: Marion <56403724+MarionBWeinzierl@users.noreply.github.com> Date: Tue, 15 Aug 2023 09:24:54 +0100 Subject: [PATCH 01/39] Update README.md - fill in empty link text strings --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 67b2aadc..bbbd2563 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ These are development notes for the package, user documentation can be found at: -[](https://pyrealm.readthedocs.io/) +[https://pyrealm.readthedocs.io/](https://pyrealm.readthedocs.io/) ## Overview @@ -21,7 +21,7 @@ development and then for package building and publication. You will need to inst The codebase is developed in `git` with a repository at: -[](https://github.com/davidorme/pyrealm) +[https://github.com/davidorme/pyrealm](https://github.com/davidorme/pyrealm) It uses the `git flow` model for development and release. Briefly: @@ -74,7 +74,7 @@ The project uses continuous integration via GitHub Actions to check that the pac building correctly and that both `doctest` and `pytest` tests are passing. The status of builds can be seen at: -[](https://github.com/davidorme/pyrealm/actions) +[https://github.com/davidorme/pyrealm/actions](https://github.com/davidorme/pyrealm/actions) ## Documentation @@ -116,7 +116,7 @@ make html The documentation for the package is hosted at: -[](https://pyrealm.readthedocs.io/en/develop/pmodel.html) +[https://pyrealm.readthedocs.io/en/develop/pmodel.html](https://pyrealm.readthedocs.io/en/develop/pmodel.html) This has been configured to build commits to the `master` branch, which should generate version specific sets of documentation. @@ -211,7 +211,7 @@ poetry publish -r test-pypi Log in to: -[](https://readthedocs.org) +[https://readthedocs.org](https://readthedocs.org) which is the admin site controlling the build process. From the Versions tab, activate the `release/new_release` branch and wait for it to build. Check the Builds tab to see From 390b1ab7c60bd15a71087dd491dfc9aba7eead36 Mon Sep 17 00:00:00 2001 From: Marion <56403724+MarionBWeinzierl@users.noreply.github.com> Date: Tue, 15 Aug 2023 10:00:43 +0100 Subject: [PATCH 02/39] extended readme with quickstart instructions --- README.md | 30 +++++++++++++++++++++++++++--- 1 file changed, 27 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index bbbd2563..ce751cd3 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,25 @@ These are development notes for the package, user documentation can be found at: This a Python 3 package intended to provide a common framework for a number of related models of plant productivity, growth and demography. +***TODO**:Add explanation what the code actually does, how it is run (standalone? coupled? what are the inputs and outputs?), and, if applicable, relevant papers* + +## Quick Start + +The code needs Python 3, version 3.9 or newer, and [Poetry](https://python-poetry.org/) for dependency management. + +With that, install the dependencies defined in [pyproject.toml](https://github.com/ImperialCollegeLondon/pyrealm/blob/develop/pyproject.toml) + +```bash +poetry install +``` +Then you can run the tests + +```bash +poetry run pytest +``` +***TODO**: Add minimum working example, i.e., how can I run a small thing myself?* +***TODO**: Add what the required inputs and expected outputs are.* + ## Code development ### Package managment @@ -19,7 +38,7 @@ development and then for package building and publication. You will need to inst ### Source code management -The codebase is developed in `git` with a repository at: +The codebase is version-controlled using `git` with a repository at: [https://github.com/davidorme/pyrealm](https://github.com/davidorme/pyrealm) @@ -105,11 +124,16 @@ included simply into the documentation. Additional python packages given in `docs/source/requirements.txt` are needed to build the documentation. To actually build the documentation, use `make` in the package root, -which will use the `Makefile` created by `sphinx-quickstart`. +which will use the `Makefile` created by `sphinx-quickstart`. *TODO: Is this paragraph still true, i.e., is it replaced by the commands below or does it still hold?* ```bash +# Install dependencies +poetry install +# Set ipython kernel +poetry run python -m ipykernel install --user --name=pyrealm_python3 +# Build docs using sphinx cd docs -make html +poetry run sphinx-build -W --keep-going source build ``` ### Online documentation From 5d23d01164c08b0a93b6e67bf5e11304de7b5a8d Mon Sep 17 00:00:00 2001 From: Marion <56403724+MarionBWeinzierl@users.noreply.github.com> Date: Tue, 15 Aug 2023 10:06:00 +0100 Subject: [PATCH 03/39] added blank line around code block in readme --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index ce751cd3..87e9102c 100644 --- a/README.md +++ b/README.md @@ -20,12 +20,15 @@ With that, install the dependencies defined in [pyproject.toml](https://github.c ```bash poetry install ``` + Then you can run the tests ```bash poetry run pytest ``` + ***TODO**: Add minimum working example, i.e., how can I run a small thing myself?* + ***TODO**: Add what the required inputs and expected outputs are.* ## Code development From d6a69c5ae18e5a596e4332123c05217e008f32cc Mon Sep 17 00:00:00 2001 From: Marion <56403724+MarionBWeinzierl@users.noreply.github.com> Date: Tue, 15 Aug 2023 10:08:59 +0100 Subject: [PATCH 04/39] Shortened lines --- README.md | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 87e9102c..84ec2c65 100644 --- a/README.md +++ b/README.md @@ -9,13 +9,17 @@ These are development notes for the package, user documentation can be found at: This a Python 3 package intended to provide a common framework for a number of related models of plant productivity, growth and demography. -***TODO**:Add explanation what the code actually does, how it is run (standalone? coupled? what are the inputs and outputs?), and, if applicable, relevant papers* +***TODO**:Add explanation what the code actually does, how it is run +(standalone? coupled? what are the inputs and outputs?), and, if applicable, +relevant papers* ## Quick Start -The code needs Python 3, version 3.9 or newer, and [Poetry](https://python-poetry.org/) for dependency management. +The code needs Python 3, version 3.9 or newer, and [Poetry](https://python-poetry.org/) +for dependency management. -With that, install the dependencies defined in [pyproject.toml](https://github.com/ImperialCollegeLondon/pyrealm/blob/develop/pyproject.toml) +With that, install the dependencies defined in +[pyproject.toml](https://github.com/ImperialCollegeLondon/pyrealm/blob/develop/pyproject.toml) ```bash poetry install @@ -127,7 +131,9 @@ included simply into the documentation. Additional python packages given in `docs/source/requirements.txt` are needed to build the documentation. To actually build the documentation, use `make` in the package root, -which will use the `Makefile` created by `sphinx-quickstart`. *TODO: Is this paragraph still true, i.e., is it replaced by the commands below or does it still hold?* +which will use the `Makefile` created by `sphinx-quickstart`. +*TODO: Is this paragraph still true, i.e., is it replaced by the commands below or does +it still hold?* ```bash # Install dependencies From 4636ace052cc224c8ff3dc03884c93c9e8a60340 Mon Sep 17 00:00:00 2001 From: MarionBWeinzierl Date: Tue, 15 Aug 2023 10:14:42 +0100 Subject: [PATCH 05/39] remove single blank spaces at the end of lines --- README.md | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 84ec2c65..d064d46e 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,6 @@ # The `pyrealm` package These are development notes for the package, user documentation can be found at: - [https://pyrealm.readthedocs.io/](https://pyrealm.readthedocs.io/) ## Overview @@ -9,16 +8,16 @@ These are development notes for the package, user documentation can be found at: This a Python 3 package intended to provide a common framework for a number of related models of plant productivity, growth and demography. -***TODO**:Add explanation what the code actually does, how it is run -(standalone? coupled? what are the inputs and outputs?), and, if applicable, +***TODO**:Add explanation what the code actually does, how it is run +(standalone? coupled? what are the inputs and outputs?), and, if applicable, relevant papers* ## Quick Start -The code needs Python 3, version 3.9 or newer, and [Poetry](https://python-poetry.org/) +The code needs Python 3, version 3.9 or newer, and [Poetry](https://python-poetry.org/) for dependency management. -With that, install the dependencies defined in +With that, install the dependencies defined in [pyproject.toml](https://github.com/ImperialCollegeLondon/pyrealm/blob/develop/pyproject.toml) ```bash @@ -131,8 +130,8 @@ included simply into the documentation. Additional python packages given in `docs/source/requirements.txt` are needed to build the documentation. To actually build the documentation, use `make` in the package root, -which will use the `Makefile` created by `sphinx-quickstart`. -*TODO: Is this paragraph still true, i.e., is it replaced by the commands below or does +which will use the `Makefile` created by `sphinx-quickstart`. +*TODO: Is this paragraph still true, i.e., is it replaced by the commands below or does it still hold?* ```bash From de6d8d4cab8a0ef286b62806073baf1547985831 Mon Sep 17 00:00:00 2001 From: Marion <56403724+MarionBWeinzierl@users.noreply.github.com> Date: Mon, 21 Aug 2023 14:01:11 +0100 Subject: [PATCH 06/39] Add info about existing worked examples in documentation --- README.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index d064d46e..158ad7b3 100644 --- a/README.md +++ b/README.md @@ -30,9 +30,11 @@ Then you can run the tests poetry run pytest ``` -***TODO**: Add minimum working example, i.e., how can I run a small thing myself?* +A code example with explanations of how to pyrealm using the P Model can be found as [worked example in the documentation](https://pyrealm.readthedocs.io/en/latest/users/pmodel/pmodel_details/worked_examples.html). There is another [worked example of the P Model with acclimatisation](https://pyrealm.readthedocs.io/en/latest/users/pmodel/subdaily_details/worked_example.html), as well as a [worked example comparing C3 plants and C4 plants](https://pyrealm.readthedocs.io/en/latest/users/pmodel/c3c4model.html#worked-example). -***TODO**: Add what the required inputs and expected outputs are.* +***TODO**: Add code for minimum working example, i.e., how can I run a small thing myself? -- Is the PModel example minimal?* + +***TODO**: Add what the required inputs and expected outputs of a general pyrealm run are.* ## Code development From 2b25347f959b1a009c218b0175f8e2e666a180f7 Mon Sep 17 00:00:00 2001 From: Marion <56403724+MarionBWeinzierl@users.noreply.github.com> Date: Mon, 21 Aug 2023 14:04:22 +0100 Subject: [PATCH 07/39] Update README.md --- README.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 158ad7b3..71666a0a 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,12 @@ Then you can run the tests poetry run pytest ``` -A code example with explanations of how to pyrealm using the P Model can be found as [worked example in the documentation](https://pyrealm.readthedocs.io/en/latest/users/pmodel/pmodel_details/worked_examples.html). There is another [worked example of the P Model with acclimatisation](https://pyrealm.readthedocs.io/en/latest/users/pmodel/subdaily_details/worked_example.html), as well as a [worked example comparing C3 plants and C4 plants](https://pyrealm.readthedocs.io/en/latest/users/pmodel/c3c4model.html#worked-example). +A code example with explanations of how to pyrealm using the P Model can be found as +[worked example in the documentation](https://pyrealm.readthedocs.io/en/latest/users/pmodel/pmodel_details/worked_examples.html). +There is another +[worked example of the P Model with acclimatisation](https://pyrealm.readthedocs.io/en/latest/users/pmodel/subdaily_details/worked_example.html), +as well as a +[worked example comparing C3 plants and C4 plants](https://pyrealm.readthedocs.io/en/latest/users/pmodel/c3c4model.html#worked-example). ***TODO**: Add code for minimum working example, i.e., how can I run a small thing myself? -- Is the PModel example minimal?* From 731fde9dce80d90e30f6fea44ce3c8b10570b0b1 Mon Sep 17 00:00:00 2001 From: Marion <56403724+MarionBWeinzierl@users.noreply.github.com> Date: Mon, 21 Aug 2023 14:06:55 +0100 Subject: [PATCH 08/39] Update README.md --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 71666a0a..a4f1cc23 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,8 @@ There is another as well as a [worked example comparing C3 plants and C4 plants](https://pyrealm.readthedocs.io/en/latest/users/pmodel/c3c4model.html#worked-example). -***TODO**: Add code for minimum working example, i.e., how can I run a small thing myself? -- Is the PModel example minimal?* +***TODO**: Add code for minimum working example, i.e., how can I run a small thing myself? +-- Is the PModel example minimal?* ***TODO**: Add what the required inputs and expected outputs of a general pyrealm run are.* From 3719c68483ca9e699e48a4effa8db5638faf7f6c Mon Sep 17 00:00:00 2001 From: Marion <56403724+MarionBWeinzierl@users.noreply.github.com> Date: Mon, 21 Aug 2023 14:08:33 +0100 Subject: [PATCH 09/39] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index a4f1cc23..579fc212 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ There is another as well as a [worked example comparing C3 plants and C4 plants](https://pyrealm.readthedocs.io/en/latest/users/pmodel/c3c4model.html#worked-example). -***TODO**: Add code for minimum working example, i.e., how can I run a small thing myself? +***TODO**: Add code for minimum working example, i.e., how can I run a small thing myself? -- Is the PModel example minimal?* ***TODO**: Add what the required inputs and expected outputs of a general pyrealm run are.* From f3a189a99abd882ec281ac7cdc13a3988f95bff5 Mon Sep 17 00:00:00 2001 From: MarionBWeinzierl Date: Mon, 21 Aug 2023 14:30:51 +0100 Subject: [PATCH 10/39] added license file --- LICENSE | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 LICENSE diff --git a/LICENSE b/LICENSE new file mode 100644 index 00000000..fc762ac2 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2023 David Orme + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. From ebe570a4bc967fbd85af1d5e20bd890f9cc01eb5 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 22 Aug 2023 10:00:42 +0100 Subject: [PATCH 11/39] Added draft CITATION.cff --- CITATION.cff | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..e01845d8 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,21 @@ +cff-version: 1.2.0 +title: pyrealm +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software +authors: + - given-names: C. David L. + family-names: Orme + email: d.orme@imperial.ac.uk + affiliation: Imperial College London + orcid: 'https://orcid.org/0000-0002-7005-1394' +repository-code: 'https://github.com/ImperialCollegeLondon/pyrealm' +url: 'https://pyrealm.readthedocs.io' +repository: 'https://pypi.org/project/pyrealm/' +abstract: >- + The pyrealm package provides an integrated set of Python 3 + modules for modelling plant productivity, growth and + demography and the estimation of growing conditions. +license: MIT + From 15c474fb0d06d5f3beac00293f8fddfb2e1622bc Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 22 Aug 2023 12:26:05 +0100 Subject: [PATCH 12/39] Simplified README.md to remove CONTRIBUTING information and add funding/support details --- README.md | 344 +++++++++--------------------------------------------- 1 file changed, 57 insertions(+), 287 deletions(-) diff --git a/README.md b/README.md index 579fc212..212ea31d 100644 --- a/README.md +++ b/README.md @@ -1,299 +1,69 @@ # The `pyrealm` package -These are development notes for the package, user documentation can be found at: -[https://pyrealm.readthedocs.io/](https://pyrealm.readthedocs.io/) +The `pyrealm` package provides a toolbox implementing some key models for estimating +plant productivity, growth and demography in Python 3. The outputs of different models +can be then easily fed into other models within `pyrealm` to allow productivity +estimates to be fed forward into estimation of net primary productivity, growth and +ultimately plant community demography. -## Overview +The `pyrealm` package currently includes: -This a Python 3 package intended to provide a common framework for a number of -related models of plant productivity, growth and demography. +* The P Model for estimating optimal rates of plant photosynthesis given the balance + between carbon capture and water loss. This includes recent extensions to incorporate + the effects of water stress, slow acclimation processes, models of C3/C4 competition + and carbon isotope fractionation. +* The T Model of the allocation of gross primary productivity to estimate net primary + productivity and hence plant growth. -***TODO**:Add explanation what the code actually does, how it is run -(standalone? coupled? what are the inputs and outputs?), and, if applicable, -relevant papers* +For more details, see the package website: +[https://pyrealm.readthedocs.io/](https://pyrealm.readthedocs.io/). -## Quick Start +**TODO** Need to link here to a _roadmap_ for the package and therefore _create_ that +roadmap along with the a feature set to aim for in version 1.0.0. -The code needs Python 3, version 3.9 or newer, and [Poetry](https://python-poetry.org/) -for dependency management. +## Using `pyrealm` -With that, install the dependencies defined in -[pyproject.toml](https://github.com/ImperialCollegeLondon/pyrealm/blob/develop/pyproject.toml) - -```bash -poetry install -``` - -Then you can run the tests - -```bash -poetry run pytest -``` - -A code example with explanations of how to pyrealm using the P Model can be found as -[worked example in the documentation](https://pyrealm.readthedocs.io/en/latest/users/pmodel/pmodel_details/worked_examples.html). -There is another -[worked example of the P Model with acclimatisation](https://pyrealm.readthedocs.io/en/latest/users/pmodel/subdaily_details/worked_example.html), -as well as a -[worked example comparing C3 plants and C4 plants](https://pyrealm.readthedocs.io/en/latest/users/pmodel/c3c4model.html#worked-example). - -***TODO**: Add code for minimum working example, i.e., how can I run a small thing myself? --- Is the PModel example minimal?* - -***TODO**: Add what the required inputs and expected outputs of a general pyrealm run are.* - -## Code development - -### Package managment - -The package uses `poetry` to manage dependencies, generate virtual environments for code -development and then for package building and publication. You will need to install -`poetry` to develop the code. - -### Source code management - -The codebase is version-controlled using `git` with a repository at: - -[https://github.com/davidorme/pyrealm](https://github.com/davidorme/pyrealm) - -It uses the `git flow` model for development and release. Briefly: - -* All code development should happen specific `feature/feature_name` branches. -* Pull requests (PR) should be made to merge feature branches into the `develop` branch. -* Candidate release versions should be made on specific `release/x.y.z` branches - and these are then committed to the `master` branch only after final checking. -* The `master` branch should only ever contain commits representing new release - versions - do not work on the `master` branch. - -Both the `develop` and `master` branches are protected on GitHub to avoid accidents! - -### Code quality - -The project uses the `pre-commit` tool to enforce code quality. The configuration file -`.pre-commit-config.yaml` shows the details of the tool chain, but `isort`, `black`, -`flake8` and `markdownlint` are used to maintain code quality. You will need to install -`pre-commit` to develop package code, and each PR must pass the same set of checks. - -### Code testing - -#### Using `doctest` - -The package docstrings contain `doctest` examples of code use. These are intended to -demonstrate use and to validate a reference set of inputs against expected outputs. They -do not provide extensive unit testing! To run the docstring tests, use: - -```bash -python -m doctest pyrealm/pmodel.py -python -m doctest pyrealm/*.py -``` - -For `doctest` on warnings, see the example for `pyrealm.utilities.convert_rh_to_vpd` -which redirects the stderr to stdout to allow for the warning text to be included in the -doctest. - -#### Using `pytest` - -The `test` directory contains `pytest` modules to provide greater testing of different -input combinations and to check errors are raised correctly. These are the main tests -that the package is behaving as expected. - -```bash -pytest -``` - -### Continuous integration - -The project uses continuous integration via GitHub Actions to check that the package is -building correctly and that both `doctest` and `pytest` tests are passing. The status of -builds can be seen at: - -[https://github.com/davidorme/pyrealm/actions](https://github.com/davidorme/pyrealm/actions) - -## Documentation - -The `pyrealm` package is documented using `sphinx`, with source material in the -`docs/source` directory. - -The documentation in `source` uses [Myst -Markdown](https://myst-parser.readthedocs.io/en/latest/) rather than the standard -`sphinx` reStructuredText (`.rst`) format. This is because the documentation uses the -`myst_nb` extension to `sphinx` that supports running documentation as a Jupyter -notebook: the built documentation includes examples of running code and output plots to -demonstrate the use and behaviour of the package. - -The `sphinx` configuration includes the `sphinx.ext.mathjax` extension to support -mathematical notation. This has been configured to also load the `mhchem` extension, -supporting the rendering of chemical notation. - -### Docstrings - -The module codes uses docstrings written in the [Google -style](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). -Unlike the main documentation pages, the docstrings in code are written using -reStructuredText because the `autodoc` functions in `sphinx` currently rely on `rst` -inputs. This allows the function documentation to be stored alongside the code and -included simply into the documentation. - -### Building the documentation - -Additional python packages given in `docs/source/requirements.txt` are needed to build -the documentation. To actually build the documentation, use `make` in the package root, -which will use the `Makefile` created by `sphinx-quickstart`. -*TODO: Is this paragraph still true, i.e., is it replaced by the commands below or does -it still hold?* - -```bash -# Install dependencies -poetry install -# Set ipython kernel -poetry run python -m ipykernel install --user --name=pyrealm_python3 -# Build docs using sphinx -cd docs -poetry run sphinx-build -W --keep-going source build -``` - -### Online documentation - -The documentation for the package is hosted at: - -[https://pyrealm.readthedocs.io/en/develop/pmodel.html](https://pyrealm.readthedocs.io/en/develop/pmodel.html) - -This has been configured to build commits to the `master` branch, which should -generate version specific sets of documentation. - -### Referencing - -The documentation uses the `sphinxcontrib-bibtex` package to support citations. -This uses Latex like citation keys in the documentation to insert references and -build a bibliography. The reference library in `source/refs.bib` needs to be -kept up to date with the literature for the project. The `sphinx_astrorefs` package is -used to provide an Author Date style citation format. - -## Release process - -Releasing a new version of the package follows the flow below: - -1. Create a `release` branch from `develop` containing the new release code. -2. Check that this branch builds correctly, that the documentation builds correctly and - that the package publishes to the `test-pypi` repository. -3. When all is well, create pull requests on GitHub to merge the `release` branch into - both `develop` and `master`, along with a version tag for the release. -4. Once you have updated your local repository, then the tag can be used to build and - publish the final version to the main PyPi site. - -It is easier if `git` is configured to push new tags along with commits. This -essentially just means that new releases can be sent with a single commit. This only -needs to be set once. - -```bash -set git config --global push.followTags true -``` - -### Create the release branch - -Using `git flow` commands as an example to create a new release: - -```sh -git flow release start new_release -``` - -Obviously, use something specific, not `new_release`! Ideally, you would do a dry run of -the next step and use the version - but it should be fairly obvious what this will be! - -The `poetry version` command can then be used to bump the version number. Note that the -command needs a 'bump rule', which sets which part of the semantic version number to -increment (`major`, `minor` or `patch`). For example: - -```sh -poetry version patch -``` - -This updates `pyproject.toml`. At present, the package is set up so that you also *have -to update the version number in `pyrealm/version.py`* to match manually. - -### Publish and test the release branch - -With those changes committed, publish the release branch: - -```sh -git commit -m "Version bump" pyrealm/version.py -git flow release publish new_release -``` - -The GitHub Actions will then ensure that the code passes quality assurance and then runs -the test suites on a range of Python versions and operating systems. - -### Check package publication - -The `sdist` and `wheel` builds for the package can then be built locally using `poetry` - -```bash -poetry build -``` - -The first time this is run, `poetry` needs to be configured to add the Test PyPi -repository and an API token from that site. Note that accounts are not shared between -the Test and main PyPi sites: the API token for `test-pypi` is different from -`pypi` and you have to log in to each system separately and generate a token on each. +The `pyrealm` package requires Python 3.9 or greater and can be installed from +[PyPi](https://pypi.org/project/pyrealm/): ```sh -poetry config repositories.test-pypi https://test.pypi.org/legacy/ -poetry config pypi-token.test-pypi +pip install pyrealm ``` -The built packages can then be published to `test-pypi` using: - -```sh -poetry publish -r test-pypi -``` - -### Check the documentation builds - -Log in to: - -[https://readthedocs.org](https://readthedocs.org) - -which is the admin site controlling the build process. From the Versions tab, activate -the `release/new_release` branch and wait for it to build. Check the Builds tab to see -that it has built successfully and maybe check updates! If it has built succesfully, do -check pages to make sure that page code has executed successfully, and then go back to -the Versions tab and deactivate and hide the branch. - -### Create pull requests into `master` and `develop` - -If all is well, then two PRs need to be made on GitHub: - -* The `release` branch into `master`, to bring all commits since the last release and - any fixes on release into `master`. -* The `release` branch into `develop`, to bring any `release` fixes back into `develop`. - -Once both of those have been merged, the `feature` branch can be deleted. - -### Tag, build and publish - -Once the `origin` repository is merged, then use `git pull` to bring `develop` and -`master` up to date on a local repo. Then, create a tag using the release version. - -```sh -git checkout master -git tag -git push --tags -``` - -The final commit on `master` is now tagged with the release version. You can add tags on -the GitHub website, but only by using the GitHub release system and we are using PyPi to -distribute package releases. - -Before publishing a package to the main PyPi site for the first time, you need to set an -API token for PyPi. - -```sh -poetry config pypi-token.pypi -``` - -And now you can build the packages from `master` and publish. - -```sh -poetry build -poetry publish -``` +At present, the package is designed for use with Python scripts or Jupyter notebooks. +Users will typically load data, using for example [`numpy`](https://numpy.org/) or +[`xarray`](https://docs.xarray.dev/en/stable/), and then import and call `pyrealm` +classes and functions. + +The package website provides worked examples of using `pyrealm`, for example to: + +* [fit the P + Model](https://pyrealm.readthedocs.io/en/latest/users/pmodel/pmodel_details/worked_examples.html), +* [include acclimation in estimating light use + efficiency](https://pyrealm.readthedocs.io/en/latest/users/pmodel/subdaily_details/worked_example.html) + , and +* [estimate C3/C4 + competition](https://pyrealm.readthedocs.io/en/latest/users/pmodel/c3c4model.html#worked-example). + +## Support and funding + +Development of the `prealm` package has been supported by the following grants and +institutions: + +* The [REALM project](https://prenticeclimategroup.wordpress.com/realm-team/), funded by + an [ERC grant](https://cordis.europa.eu/project/id/787203) to Prof. Colin Prentice + (Imperial College London). +* The [LEMONTREE project](https://research.reading.ac.uk/lemontree/), funded by Schmidt + Futures through the [VESRI + programme](https://www.schmidtfutures.com/our-work/virtual-earth-system-research-institute-vesri/) + to support an international research team lead by Prof. Sandy Harrison (University of + Reading). +* The [Virtual Rainforest project](https://pyrealm.readthedocs.io/), funded by a + Distinguished Scientist award from the [NOMIS + Foundation](https://nomisfoundation.ch/research-projects/a-virtual-rainforest-for-understanding-the-stability-resilience-and-sustainability-of-complex-ecosystems/) + to Prof. Robert Ewers (Imperial College London) +* Research software engineering support from the [Institute of Computing for Climate + Science](https://iccs.cam.ac.uk/) at the University of Cambridge, through the [Virtual + Institute for Scientific + Software](https://www.schmidtfutures.com/our-work/virtual-institute-for-scientific-software/) + program funded by Schmidt Futures. From c45330c07bfc2feca853bc521bb677a864bd38c2 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 22 Aug 2023 12:49:20 +0100 Subject: [PATCH 13/39] First draft of CONTRIBUTING.md --- CONTRIBUTING.md | 291 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 291 insertions(+) create mode 100644 CONTRIBUTING.md diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..406bb98b --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,291 @@ +# Contributing to the `pyrealm` package + +## Quick Start + +The code needs Python 3, version 3.9 or newer. The `pyrealm` package can be installed +from [PyPi](https://pypi.org/project/pyrealm/) but to develop the package you will need +to clone this repository and then install +[Poetry](https://python-poetry.org/docs/#installation) for dependency management and to +set up the development environment. + +From within the cloned repository, first install the dependencies defined in +[pyproject.toml](https://github.com/ImperialCollegeLondon/pyrealm/blob/develop/pyproject.toml) + +```bash +poetry install +``` + +Then you can run the tests + +```bash +poetry run pytest +``` + +## Example usage + +The package is designed to provide a set of tools to be used within a Python script or +notebook. The package website provides some minimal examples of using the various +modules within `pyrealm` - see the [README](README.md#using-pyrealm) for links to those +pages - but typically a user will load input data, pass it into imported `pyrealm` +classes and functions and then use the outputs in further functions. + +Some of the package modules - such as the `pmodel` and `splash` modules - require input +data in arrays, typically with spatial and temporal dimensions loaded from NetCDF files +or similar formats. Other modules - such as the `tmodel` - work on a site by site basis +and require the configuration of site-specific details. + +## Code development + +### Package managment + +The package uses `poetry` to manage dependencies, generate virtual environments for code +development and then for package building and publication. You will need to install +`poetry` to develop the code. + +### Source code management + +The codebase is version-controlled using `git` with a repository at: + +[https://github.com/ImperialCollegeLondon/pyrealm](https://github.com/ImperialCollegeLondon/pyrealm) + +The package uses the `git flow` model for development and release: + +* All code development should happen specific `feature/feature_name` branches. +* Pull requests (PR) should be made to merge feature branches into the `develop` branch. +* Candidate release versions should be made on specific `release/x.y.z` branches + and these are then committed to the `master` branch only after final checking. +* The `master` branch should only ever contain commits representing new release + versions - do not work on the `master` branch. + +Both the `develop` and `master` branches are protected on GitHub to avoid accidents! + +### Code quality + +The project uses the `pre-commit` tool to enforce code quality. The configuration file +`.pre-commit-config.yaml` shows the details of the tool chain, but `isort`, `black`, +`flake8` and `markdownlint` are used to maintain code quality. You will need to install +`pre-commit` to develop package code, and each PR must pass the same set of checks. + +### Code testing + +#### Using `doctest` + +The package docstrings contain `doctest` examples of code use. These are intended to +demonstrate use and to validate a reference set of inputs against expected outputs. They +do not provide extensive unit testing! To run the docstring tests, use: + +```bash +python -m doctest pyrealm/pmodel.py +python -m doctest pyrealm/*.py +``` + +For `doctest` on warnings, see the example for `pyrealm.utilities.convert_rh_to_vpd` +which redirects the stderr to stdout to allow for the warning text to be included in the +doctest. + +#### Using `pytest` + +The `test` directory contains `pytest` modules to provide greater testing of different +input combinations and to check errors are raised correctly. These are the main tests +that the package is behaving as expected. + +```bash +pytest +``` + +### Continuous integration + +The project uses continuous integration via GitHub Actions to check that the package is +building correctly and that both `doctest` and `pytest` tests are passing. The status of +builds can be seen at: + +[https://github.com/davidorme/pyrealm/actions](https://github.com/davidorme/pyrealm/actions) + +## Documentation + +The `pyrealm` package is documented using `sphinx`, with source material in the +`docs/source` directory. + +The documentation in `source` uses [Myst +Markdown](https://myst-parser.readthedocs.io/en/latest/) rather than the standard +`sphinx` reStructuredText (`.rst`) format. This is because the documentation uses the +`myst_nb` extension to `sphinx` that supports running documentation as a Jupyter +notebook: the built documentation includes examples of running code and output plots to +demonstrate the use and behaviour of the package. + +The `sphinx` configuration includes the `sphinx.ext.mathjax` extension to support +mathematical notation. This has been configured to also load the `mhchem` extension, +supporting the rendering of chemical notation. + +### Docstrings + +The module codes uses docstrings written in the [Google +style](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). +Unlike the main documentation pages, the docstrings in code are written using +reStructuredText because the `autodoc` functions in `sphinx` currently rely on `rst` +inputs. This allows the function documentation to be stored alongside the code and +included simply into the documentation. + +### Building the documentation + +Additional python packages given in `docs/source/requirements.txt` are needed to build +the documentation. To actually build the documentation, use `make` in the package root, +which will use the `Makefile` created by `sphinx-quickstart`. +*TODO: Is this paragraph still true, i.e., is it replaced by the commands below or does +it still hold?* + +```bash +# Install dependencies +poetry install +# Set ipython kernel +poetry run python -m ipykernel install --user --name=pyrealm_python3 +# Build docs using sphinx +cd docs +poetry run sphinx-build -W --keep-going source build +``` + +### Online documentation + +The documentation for the package is hosted at: + +[https://pyrealm.readthedocs.io/en/develop/pmodel.html](https://pyrealm.readthedocs.io/en/develop/pmodel.html) + +This has been configured to build commits to the `master` branch, which should +generate version specific sets of documentation. + +### Referencing + +The documentation uses the `sphinxcontrib-bibtex` package to support citations. +This uses Latex like citation keys in the documentation to insert references and +build a bibliography. The reference library in `source/refs.bib` needs to be +kept up to date with the literature for the project. The `sphinx_astrorefs` package is +used to provide an Author Date style citation format. + +## Release process + +Releasing a new version of the package follows the flow below: + +1. Create a `release` branch from `develop` containing the new release code. +2. Check that this branch builds correctly, that the documentation builds correctly and + that the package publishes to the `test-pypi` repository. +3. When all is well, create pull requests on GitHub to merge the `release` branch into + both `develop` and `master`, along with a version tag for the release. +4. Once you have updated your local repository, then the tag can be used to build and + publish the final version to the main PyPi site. + +It is easier if `git` is configured to push new tags along with commits. This +essentially just means that new releases can be sent with a single commit. This only +needs to be set once. + +```bash +set git config --global push.followTags true +``` + +### Create the release branch + +Using `git flow` commands as an example to create a new release: + +```sh +git flow release start new_release +``` + +Obviously, use something specific, not `new_release`! Ideally, you would do a dry run of +the next step and use the version - but it should be fairly obvious what this will be! + +The `poetry version` command can then be used to bump the version number. Note that the +command needs a 'bump rule', which sets which part of the semantic version number to +increment (`major`, `minor` or `patch`). For example: + +```sh +poetry version patch +``` + +This updates `pyproject.toml`. At present, the package is set up so that you also *have +to update the version number in `pyrealm/version.py`* to match manually. + +### Publish and test the release branch + +With those changes committed, publish the release branch: + +```sh +git commit -m "Version bump" pyrealm/version.py +git flow release publish new_release +``` + +The GitHub Actions will then ensure that the code passes quality assurance and then runs +the test suites on a range of Python versions and operating systems. + +### Check package publication + +The `sdist` and `wheel` builds for the package can then be built locally using `poetry` + +```bash +poetry build +``` + +The first time this is run, `poetry` needs to be configured to add the Test PyPi +repository and an API token from that site. Note that accounts are not shared between +the Test and main PyPi sites: the API token for `test-pypi` is different from +`pypi` and you have to log in to each system separately and generate a token on each. + +```sh +poetry config repositories.test-pypi https://test.pypi.org/legacy/ +poetry config pypi-token.test-pypi +``` + +The built packages can then be published to `test-pypi` using: + +```sh +poetry publish -r test-pypi +``` + +### Check the documentation builds + +Log in to: + +[https://readthedocs.org](https://readthedocs.org) + +which is the admin site controlling the build process. From the Versions tab, activate +the `release/new_release` branch and wait for it to build. Check the Builds tab to see +that it has built successfully and maybe check updates! If it has built succesfully, do +check pages to make sure that page code has executed successfully, and then go back to +the Versions tab and deactivate and hide the branch. + +### Create pull requests into `master` and `develop` + +If all is well, then two PRs need to be made on GitHub: + +* The `release` branch into `master`, to bring all commits since the last release and + any fixes on release into `master`. +* The `release` branch into `develop`, to bring any `release` fixes back into `develop`. + +Once both of those have been merged, the `feature` branch can be deleted. + +### Tag, build and publish + +Once the `origin` repository is merged, then use `git pull` to bring `develop` and +`master` up to date on a local repo. Then, create a tag using the release version. + +```sh +git checkout master +git tag +git push --tags +``` + +The final commit on `master` is now tagged with the release version. You can add tags on +the GitHub website, but only by using the GitHub release system and we are using PyPi to +distribute package releases. + +Before publishing a package to the main PyPi site for the first time, you need to set an +API token for PyPi. + +```sh +poetry config pypi-token.pypi +``` + +And now you can build the packages from `master` and publish. + +```sh +poetry build +poetry publish +``` From 6a930bac1123ee276334bc01cc51daa584a9c2e5 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 22 Aug 2023 12:57:03 +0100 Subject: [PATCH 14/39] Updating master to main in CONTRIBUTING --- CONTRIBUTING.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 406bb98b..592865e5 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -53,11 +53,11 @@ The package uses the `git flow` model for development and release: * All code development should happen specific `feature/feature_name` branches. * Pull requests (PR) should be made to merge feature branches into the `develop` branch. * Candidate release versions should be made on specific `release/x.y.z` branches - and these are then committed to the `master` branch only after final checking. -* The `master` branch should only ever contain commits representing new release - versions - do not work on the `master` branch. + and these are then committed to the `main` branch only after final checking. +* The `main` branch should only ever contain commits representing new release + versions - do not work on the `main` branch. -Both the `develop` and `master` branches are protected on GitHub to avoid accidents! +Both the `develop` and `main` branches are protected on GitHub to avoid accidents! ### Code quality @@ -150,7 +150,7 @@ The documentation for the package is hosted at: [https://pyrealm.readthedocs.io/en/develop/pmodel.html](https://pyrealm.readthedocs.io/en/develop/pmodel.html) -This has been configured to build commits to the `master` branch, which should +This has been configured to build commits to the `main` branch, which should generate version specific sets of documentation. ### Referencing @@ -169,7 +169,7 @@ Releasing a new version of the package follows the flow below: 2. Check that this branch builds correctly, that the documentation builds correctly and that the package publishes to the `test-pypi` repository. 3. When all is well, create pull requests on GitHub to merge the `release` branch into - both `develop` and `master`, along with a version tag for the release. + both `develop` and `main`, along with a version tag for the release. 4. Once you have updated your local repository, then the tag can be used to build and publish the final version to the main PyPi site. @@ -251,12 +251,12 @@ that it has built successfully and maybe check updates! If it has built succesfu check pages to make sure that page code has executed successfully, and then go back to the Versions tab and deactivate and hide the branch. -### Create pull requests into `master` and `develop` +### Create pull requests into `main` and `develop` If all is well, then two PRs need to be made on GitHub: -* The `release` branch into `master`, to bring all commits since the last release and - any fixes on release into `master`. +* The `release` branch into `main`, to bring all commits since the last release and + any fixes on release into `main`. * The `release` branch into `develop`, to bring any `release` fixes back into `develop`. Once both of those have been merged, the `feature` branch can be deleted. @@ -264,15 +264,15 @@ Once both of those have been merged, the `feature` branch can be deleted. ### Tag, build and publish Once the `origin` repository is merged, then use `git pull` to bring `develop` and -`master` up to date on a local repo. Then, create a tag using the release version. +`main` up to date on a local repo. Then, create a tag using the release version. ```sh -git checkout master +git checkout main git tag git push --tags ``` -The final commit on `master` is now tagged with the release version. You can add tags on +The final commit on `main` is now tagged with the release version. You can add tags on the GitHub website, but only by using the GitHub release system and we are using PyPi to distribute package releases. @@ -283,7 +283,7 @@ API token for PyPi. poetry config pypi-token.pypi ``` -And now you can build the packages from `master` and publish. +And now you can build the packages from `main` and publish. ```sh poetry build From 19c32926164721ca06b40f28c369d3bea64fec08 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 22 Aug 2023 16:22:35 +0100 Subject: [PATCH 15/39] Removed outdated docs requirements.txt --- docs/source/requirements.txt | 8 -------- 1 file changed, 8 deletions(-) delete mode 100644 docs/source/requirements.txt diff --git a/docs/source/requirements.txt b/docs/source/requirements.txt deleted file mode 100644 index b187cdf9..00000000 --- a/docs/source/requirements.txt +++ /dev/null @@ -1,8 +0,0 @@ -sphinx==4.2.0 -sphinxcontrib-bibtex -sphinx-rtd-theme -sphinx-astrorefs -recommonmark -autodocsumm -myst_nb -matplotlib \ No newline at end of file From dacefb7a6ccd695708ed0f9aa63bdad83df939e5 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 22 Aug 2023 16:22:49 +0100 Subject: [PATCH 16/39] Updated CONTRIBUTING.md --- CONTRIBUTING.md | 184 ++++++++++++++++++++++++++++++------------------ 1 file changed, 117 insertions(+), 67 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 592865e5..e3665bf4 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,26 +2,28 @@ ## Quick Start -The code needs Python 3, version 3.9 or newer. The `pyrealm` package can be installed +### Installation + +The package requires Python 3.9 or newer. The `pyrealm` package can be installed from [PyPi](https://pypi.org/project/pyrealm/) but to develop the package you will need to clone this repository and then install [Poetry](https://python-poetry.org/docs/#installation) for dependency management and to set up the development environment. From within the cloned repository, first install the dependencies defined in -[pyproject.toml](https://github.com/ImperialCollegeLondon/pyrealm/blob/develop/pyproject.toml) +[pyproject.toml](https://github.com/ImperialCollegeLondon/pyrealm/blob/develop/pyproject.toml): ```bash poetry install ``` -Then you can run the tests +Then you can run the tests to check that the installation is working correctly: ```bash poetry run pytest ``` -## Example usage +### Example package usage The package is designed to provide a set of tools to be used within a Python script or notebook. The package website provides some minimal examples of using the various @@ -32,15 +34,16 @@ classes and functions and then use the outputs in further functions. Some of the package modules - such as the `pmodel` and `splash` modules - require input data in arrays, typically with spatial and temporal dimensions loaded from NetCDF files or similar formats. Other modules - such as the `tmodel` - work on a site by site basis -and require the configuration of site-specific details. +and require the configuration of site-specific details, such as the definition of plant +functional types and plant community structures. ## Code development -### Package managment +### Package management The package uses `poetry` to manage dependencies, generate virtual environments for code development and then for package building and publication. You will need to install -`poetry` to develop the code. +`poetry>=1.2.0` to develop the code. ### Source code management @@ -59,86 +62,133 @@ The package uses the `git flow` model for development and release: Both the `develop` and `main` branches are protected on GitHub to avoid accidents! -### Code quality +## Code documentation -The project uses the `pre-commit` tool to enforce code quality. The configuration file -`.pre-commit-config.yaml` shows the details of the tool chain, but `isort`, `black`, -`flake8` and `markdownlint` are used to maintain code quality. You will need to install -`pre-commit` to develop package code, and each PR must pass the same set of checks. +### Docstrings -### Code testing +The module codes uses docstrings written in the [Google +style](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). +Unlike the main documentation pages, the docstrings in code are written using +reStructuredText because the `autodoc` functions in `sphinx` currently rely on `rst` +inputs. This allows the function documentation to be stored alongside the code and +included simply into the documentation. -#### Using `doctest` +### Package website and documentation -The package docstrings contain `doctest` examples of code use. These are intended to -demonstrate use and to validate a reference set of inputs against expected outputs. They -do not provide extensive unit testing! To run the docstring tests, use: +The `pyrealm` package is documented using `sphinx`, with source material in the +`docs/source` directory. -```bash -python -m doctest pyrealm/pmodel.py -python -m doctest pyrealm/*.py -``` +The documentation in `source` uses [Myst +Markdown](https://myst-parser.readthedocs.io/en/latest/) rather than the standard +`sphinx` reStructuredText (`.rst`) format. This is because the documentation uses the +`myst_nb` extension to `sphinx` that supports running documentation as a Jupyter +notebook: the built documentation includes examples of running code and output plots to +demonstrate the use and behaviour of the package. -For `doctest` on warnings, see the example for `pyrealm.utilities.convert_rh_to_vpd` -which redirects the stderr to stdout to allow for the warning text to be included in the -doctest. +The `sphinx` configuration includes the `sphinx.ext.mathjax` extension to support +mathematical notation. This has been configured to also load the `mhchem` extension, +supporting the rendering of chemical notation. -#### Using `pytest` +## Code quality and continuous integration + +The project uses continuous integration (CI) via GitHub Actions to maintain code quality +and check confirm that the package and website are building correctly. The +[`pyrealm_ci.yaml`](.github/workflows/pyrealm_ci.yaml) currently defines three CI jobs: -The `test` directory contains `pytest` modules to provide greater testing of different -input combinations and to check errors are raised correctly. These are the main tests -that the package is behaving as expected. +* code quality assurance (`qa`) +* code testing (`test`) +* documentation building (`docs_build`) + +The status of code checking for pushed commits can be seen at: + +[https://github.com/ImperialCollegeLondon/pyrealm/actions](https://github.com/ImperialCollegeLondon/pyrealm/actions) + +Although GitHub Actions automates these steps for any pushes, pull requests and releases +on the repository, you should also perform the same steps locally before submitting code +to ensure that your code passes testing. + +### Code quality assurance + +The project uses `pre-commit` to enforce code quality. The configuration file +[`.pre-commit-config.yaml`](.pre-commit-config.yaml) shows the details of the tool +chain, but `isort`, `black`, `flake8` and `markdownlint` are used to maintain code +quality. + +You will need to [install `pre-commit`](https://pre-commit.com/#install) to develop +package code. Once you have installed `pre-commit` you then need to install the +configuration for the repository: ```bash -pytest +pre-commit install ``` -### Continuous integration +After this step, all commits within the repository must then pass the suite of quality +assurance checks. Note that the repository also uses a separate GitHub action to update +the code quality assurance toolchain on a weekly basis, so you will periodically see +updates to the checking. -The project uses continuous integration via GitHub Actions to check that the package is -building correctly and that both `doctest` and `pytest` tests are passing. The status of -builds can be seen at: +### Code testing -[https://github.com/davidorme/pyrealm/actions](https://github.com/davidorme/pyrealm/actions) +The `pyrealm` package principally uses `pytest` to provide benchmark tests, unit tests +and integration testing. In addition, `doctest` is used to maintain examples of code +usage in the package docstrings and ensure that the documented return values are +correct. -## Documentation +#### Using `pytest` -The `pyrealm` package is documented using `sphinx`, with source material in the -`docs/source` directory. +The `test` directory contains modules providing test suites for each of the different +package modules. This includes: -The documentation in `source` uses [Myst -Markdown](https://myst-parser.readthedocs.io/en/latest/) rather than the standard -`sphinx` reStructuredText (`.rst`) format. This is because the documentation uses the -`myst_nb` extension to `sphinx` that supports running documentation as a Jupyter -notebook: the built documentation includes examples of running code and output plots to -demonstrate the use and behaviour of the package. +* benchmark testing the output of `pyrealm` code against previously existing + implementations of some functionality, such as the `rpmodel` and `SPLASH` packages. +* unit testing of individual functions and methodsm and, +* integration testing of using combinations of modules. -The `sphinx` configuration includes the `sphinx.ext.mathjax` extension to support -mathematical notation. This has been configured to also load the `mhchem` extension, -supporting the rendering of chemical notation. +These are the main tests that the package is behaving as expected and producing stable +outputs and can be run from repository using: -### Docstrings +```bash +poetry run pytest +``` -The module codes uses docstrings written in the [Google -style](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). -Unlike the main documentation pages, the docstrings in code are written using -reStructuredText because the `autodoc` functions in `sphinx` currently rely on `rst` -inputs. This allows the function documentation to be stored alongside the code and -included simply into the documentation. +#### Using `doctest` + +The package docstrings contain `doctest` examples of code use. These examples are +intended to provide simple examples of method or function use and generate an output and +the `doctest` process is used to validate that the provided values are correct. + +These tests are automatically run when `pytest` is run, but individual module files can +be checked using, for example: + +```bash +poetry run python -m doctest pyrealm/pmodel/pmodel.py +``` + +Normally, `doctest` is used to test a return value but can also be used to check that an +error or warning is raised. See the example for `pyrealm.utilities.convert_rh_to_vpd` +which redirects the stderr to stdout to allow for the warning text to be included in the +doctest. ### Building the documentation -Additional python packages given in `docs/source/requirements.txt` are needed to build -the documentation. To actually build the documentation, use `make` in the package root, -which will use the `Makefile` created by `sphinx-quickstart`. -*TODO: Is this paragraph still true, i.e., is it replaced by the commands below or does -it still hold?* +`sphinx` is used to build an HTML version of the package documentation provided in +`docs/source` and to build the API documentation provided in the code docstrings. The +`sphinx` building process requires some extra packages, but these are included in the +`docs` group in `pyproject.toml` and should be installed. + +In order to build the package documentation, Jupyter needs to be able to associate the +documentation files with the Python environment managed by `poetry`. This is done by +installing the `poetry` environment as a new Jupyter kernel with a fixed name. This +allows all build systems to run notebooks using the correct build environment: ```bash -# Install dependencies -poetry install # Set ipython kernel poetry run python -m ipykernel install --user --name=pyrealm_python3 +``` + +In order to build the package documentation, the following command can be used: + +```bash # Build docs using sphinx cd docs poetry run sphinx-build -W --keep-going source build @@ -150,16 +200,16 @@ The documentation for the package is hosted at: [https://pyrealm.readthedocs.io/en/develop/pmodel.html](https://pyrealm.readthedocs.io/en/develop/pmodel.html) -This has been configured to build commits to the `main` branch, which should -generate version specific sets of documentation. +This has been configured to automatically build commits to the `main` branch, which +should generate version specific sets of documentation. ### Referencing -The documentation uses the `sphinxcontrib-bibtex` package to support citations. -This uses Latex like citation keys in the documentation to insert references and -build a bibliography. The reference library in `source/refs.bib` needs to be -kept up to date with the literature for the project. The `sphinx_astrorefs` package is -used to provide an Author Date style citation format. +The documentation uses the `sphinxcontrib-bibtex` package to support citations. This +uses Latex like citation keys in the documentation to insert references and build a +bibliography. The `sphinx` configuration in `docs/source/conf.py` provides a custom +Author/Year citation style. The reference library in `source/refs.bib` needs to be kept +up to date with the literature for the project. ## Release process From 6d2de440886d8fb91d55c68acea8dbb39976f87a Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 22 Aug 2023 16:25:07 +0100 Subject: [PATCH 17/39] Added contributors link to README --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 212ea31d..0d4a50e9 100644 --- a/README.md +++ b/README.md @@ -45,6 +45,11 @@ The package website provides worked examples of using `pyrealm`, for example to: * [estimate C3/C4 competition](https://pyrealm.readthedocs.io/en/latest/users/pmodel/c3c4model.html#worked-example). +## Developing `pyrealm` + +If you are interested in contributing to the development of `pyrealm`, please read the +[guide for contributors](./CONTRIBUTING.md). + ## Support and funding Development of the `prealm` package has been supported by the following grants and From b7a83c291f6db79ab2ef1c87d474c5fb5bac73aa Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 22 Aug 2023 20:50:04 +0100 Subject: [PATCH 18/39] Minor edit from Marion --- CONTRIBUTING.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index e3665bf4..0f496840 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -26,9 +26,9 @@ poetry run pytest ### Example package usage The package is designed to provide a set of tools to be used within a Python script or -notebook. The package website provides some minimal examples of using the various -modules within `pyrealm` - see the [README](README.md#using-pyrealm) for links to those -pages - but typically a user will load input data, pass it into imported `pyrealm` +notebook. The package documentation provides some minimal examples of using the various +modules within `pyrealm` - see the [README](README.md#using-pyrealm) for links to these +examples - but typically a user will load input data, pass it into imported `pyrealm` classes and functions and then use the outputs in further functions. Some of the package modules - such as the `pmodel` and `splash` modules - require input From 7e17933fbab906a858c62992c7edf86b6813b424 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 22 Aug 2023 21:04:09 +0100 Subject: [PATCH 19/39] Fixing pre-commit issues and updating pre-commit config --- .pre-commit-config.yaml | 8 ++++---- docs/source/users/pmodel/pmodel_details/extreme_values.md | 4 ++-- pyrealm/constants/base.py | 3 ++- 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ea40b507..de1b92c9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,21 +10,21 @@ repos: - id: isort additional_dependencies: [toml] - repo: https://github.com/psf/black - rev: "23.1.0" + rev: "23.7.0" hooks: - id: black - repo: https://github.com/PyCQA/flake8 - rev: 6.0.0 + rev: 6.1.0 hooks: - id: flake8 additional_dependencies: [flake8-docstrings] - repo: https://github.com/pre-commit/mirrors-mypy - rev: "v1.0.1" + rev: "v1.5.1" hooks: - id: mypy additional_dependencies: [numpy, types-tabulate] - repo: https://github.com/igorshubovych/markdownlint-cli - rev: v0.33.0 + rev: v0.35.0 hooks: - id: markdownlint diff --git a/docs/source/users/pmodel/pmodel_details/extreme_values.md b/docs/source/users/pmodel/pmodel_details/extreme_values.md index 76667e7a..c13b09a9 100644 --- a/docs/source/users/pmodel/pmodel_details/extreme_values.md +++ b/docs/source/users/pmodel/pmodel_details/extreme_values.md @@ -18,7 +18,7 @@ The four photosynthetic environment variables and the effect of temperature on t temperature dependence of quantum yield efficiency are all calculated directly from the input forcing variables. While the majority of those calculations behave smoothly with extreme values of temperature and atmospheric pressure, the calculation of the relative -viscosity of water ($\eta^*$) does not handle low temperatures well. +viscosity of water ($\eta^{\ast}$) does not handle low temperatures well. Forcing datasets for the input to the P Model - particularly remotely sensed datasets - often contain extreme values that may lead to unexpected model predictions. This page @@ -85,7 +85,7 @@ pyplot.show() The photorespiratory compensation point ($\Gamma^*$) varies with as a function of temperature and atmospheric pressure, and behaves smoothly with extreme inputs. Note -that again, $\Gamma^*$ has non-zero values for sub-zero temperatures. +that again, $\Gamma^_$ has non-zero values for sub-zero temperatures. ```{code-cell} :tags: [hide-input] diff --git a/pyrealm/constants/base.py b/pyrealm/constants/base.py index 82ee0c4b..4c14cfaf 100644 --- a/pyrealm/constants/base.py +++ b/pyrealm/constants/base.py @@ -22,11 +22,12 @@ import json -from dataclasses import asdict +from dataclasses import asdict, dataclass from dacite.core import from_dict +@dataclass(frozen=True) class ConstantsClass: """Base class for model constants. From 45ddcd2a3089513532ecd65f73a5815d3b1d4659 Mon Sep 17 00:00:00 2001 From: David Orme Date: Wed, 23 Aug 2023 10:36:13 +0100 Subject: [PATCH 20/39] Updated pytest config, fixing broken doctests --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 1a7d1d12..aad68107 100644 --- a/setup.cfg +++ b/setup.cfg @@ -33,7 +33,7 @@ addopts = --doctest-modules --ignore=pyrealm/__main__.py --ignore=tests/pmodel/generate_test_inputs.py -testpaths = tests +testpaths = tests pyrealm python_files = test_*.py [mypy] From ee7df50f83d37767d4633f28d92e635054288d4c Mon Sep 17 00:00:00 2001 From: David Orme Date: Wed, 23 Aug 2023 10:36:43 +0100 Subject: [PATCH 21/39] Fixing doctests in pmodel.functions --- pyrealm/pmodel/functions.py | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/pyrealm/pmodel/functions.py b/pyrealm/pmodel/functions.py index f65a160d..ccaea951 100644 --- a/pyrealm/pmodel/functions.py +++ b/pyrealm/pmodel/functions.py @@ -50,7 +50,7 @@ def calc_density_h2o( # It doesn't make sense to use this function for tc < 0, but in particular # the calculation shows wild numeric instability between -44 and -46 that # leads to numerous downstream issues - see the extreme values documentation. - if safe and np.nanmin(tc) < -30: + if safe and np.nanmin(tc) < np.array([-30]): raise ValueError( "Water density calculations below about -30°C are " "unstable. See argument safe to calc_density_h2o" @@ -493,8 +493,9 @@ def calc_kp_c4( Examples: >>> # Michaelis-Menten coefficient at 20 degrees Celsius and standard >>> # atmosphere (in Pa): - >>> round(calc_kp_c4(20, 101325), 5) - 9.26352 + >>> import numpy as np + >>> calc_kp_c4(np.array([20]), np.array([101325])).round(5) + array([12.46385]) """ # Check inputs, return shape not used @@ -566,10 +567,9 @@ def calc_soilmstress_stocker( A numeric value or values for :math:`\beta` Examples: - >>> # Relative reduction (%) in GPP due to soil moisture stress at - >>> # relative soil water content ('soilm') of 0.2: - >>> round((calc_soilmstress(0.2) - 1) * 100, 5) - -11.86667 + >>> # Proportion of well-watered GPP available at soil moisture of 0.2 + >>> calc_soilmstress_stocker(np.array([0.2])).round(5) + array([0.88133]) """ # TODO - move soilm params into standalone param class for this function - @@ -645,7 +645,11 @@ def calc_soilmstress_mengoli( A numeric value or values for :math:`f(\theta)` Examples: - >>> TODO + >>> import numpy as np + >>> # Proportion of well-watered GPP available with soil moisture and aridity + >>> # index values of 0.6 + >>> calc_soilmstress_mengoli(np.array([0.6]), np.array([0.6])).round(5) + array([0.78023]) """ # TODO - move soilm params into standalone param class for this function - From d7eff8b276cd69de31d13b1295fa4676c7426ea7 Mon Sep 17 00:00:00 2001 From: David Orme Date: Wed, 23 Aug 2023 10:37:14 +0100 Subject: [PATCH 22/39] Fixing doctests in pmodel.isotopes --- pyrealm/pmodel/isotopes.py | 49 ++++++++++++++++++++++++-------------- 1 file changed, 31 insertions(+), 18 deletions(-) diff --git a/pyrealm/pmodel/isotopes.py b/pyrealm/pmodel/isotopes.py index 8531dc45..db69242a 100644 --- a/pyrealm/pmodel/isotopes.py +++ b/pyrealm/pmodel/isotopes.py @@ -106,15 +106,18 @@ def calc_c4_discrimination(self, pmodel: PModel) -> None: :cite:p:`lavergne:2022a`. Examples: - >>> ppar = PModelParams(beta_cost_ratio_c4=35) - >>> env = PModelEnvironment(tc=20, patm=101325, co2=400, - ... vpd=1000, const=ppar) + >>> import numpy as np + >>> from pyrealm.pmodel import PModel, PModelEnvironment + >>> from pyrealm.constants import PModelConst + >>> const = PModelConst(beta_cost_ratio_c4=35) + >>> env = PModelEnvironment(tc=np.array([20]), patm=np.array([101325]), + ... co2=np.array([400]), vpd=np.array([1000]), const=const) >>> mod_c4 = PModel(env, method_optchi='c4_no_gamma') >>> mod_c4_delta = CalcCarbonIsotopes(mod_c4, d13CO2= -8.4, D14CO2 = 19.2) - >>> round(mod_c4_delta.Delta13C, 4) - 5.6636 - >>> round(mod_c4_delta.d13C_leaf, 4) - -13.9844 + >>> mod_c4_delta.Delta13C.round(4) + array([5.6636]) + >>> mod_c4_delta.d13C_leaf.round(4) + array([-13.9844]) """ # Equation from C3/C4 paper @@ -136,13 +139,18 @@ def calc_c4_discrimination_vonC(self, pmodel: PModel) -> None: sensitive correction term is provided in commented code but not used. Examples: - >>> ppar = PModelParams(beta_cost_ratio_c4=35) - >>> env = PModelEnvironment(tc=20, patm=101325, co2=400, - ... vpd=1000, const=ppar) + >>> import numpy as np + >>> from pyrealm.pmodel import PModel, PModelEnvironment + >>> from pyrealm.constants import PModelConst + >>> const = PModelConst(beta_cost_ratio_c4=35) + >>> env = PModelEnvironment(tc=np.array([20]), patm=np.array([101325]), + ... co2=np.array([400]), vpd=np.array([1000]), const=const) >>> mod_c4 = PModel(env, method_optchi='c4_no_gamma') >>> mod_c4_delta = CalcCarbonIsotopes(mod_c4, d13CO2= -8.4, D14CO2 = 19.2) - >>> # round(mod_c4_delta.Delta13C, 4) # NOT CHECKED 5.2753 - >>> # round(mod_c4_delta.d13C_leaf, 4) # NOT CHECKED -13.6036 + >>> # mod_c4_delta.Delta13C.round(4) + >>> # array([5.2753]) + >>> # mod_c4_delta.d13C_leaf.round(4) + >>> # array([-13.6036]) """ warn("This method is experimental code from Alienor Lavergne") @@ -173,14 +181,19 @@ def calc_c3_discrimination(self, pmodel: PModel) -> None: effect following :cite:p:`farquhar:1982a`. Examples: - >>> env = PModelEnvironment(tc=20, patm=101325, co2=400, - ... vpd=1000, theta=0.4) + >>> import numpy as np + >>> from pyrealm.pmodel import PModel, PModelEnvironment + >>> env = PModelEnvironment( + ... tc=np.array([20]), patm=np.array([101325]), + ... co2=np.array([400]), vpd=np.array([1000]), + ... theta=np.array([0.4]) + ... ) >>> mod_c3 = PModel(env, method_optchi='lavergne20_c3') >>> mod_c3_delta = CalcCarbonIsotopes(mod_c3, d13CO2= -8.4, D14CO2 = 19.2) - >>> round(mod_c3_delta.Delta13C, 4) - 20.4056 - >>> round(mod_c3_delta.d13C_leaf, 4) - -28.2296 + >>> mod_c3_delta.Delta13C.round(4) + array([20.4056]) + >>> mod_c3_delta.d13C_leaf.round(4) + array([-28.2296]) """ # 13C discrimination (permil): Farquhar et al. (1982) From 05d766789902d92d710f2ba34cf73aec89897403 Mon Sep 17 00:00:00 2001 From: David Orme Date: Wed, 23 Aug 2023 10:37:43 +0100 Subject: [PATCH 23/39] Fixing doctests in pmodel.pmodel --- pyrealm/pmodel/pmodel.py | 176 ++++++++++++++++++++++----------------- 1 file changed, 101 insertions(+), 75 deletions(-) diff --git a/pyrealm/pmodel/pmodel.py b/pyrealm/pmodel/pmodel.py index 0eb83ff4..083dbf08 100644 --- a/pyrealm/pmodel/pmodel.py +++ b/pyrealm/pmodel/pmodel.py @@ -109,14 +109,14 @@ def __init__( """Atmospheric pressure, Pa""" # Guard against calc_density issues - if np.nanmin(self.tc) < -25: + if np.nanmin(self.tc) < np.array([-25]): raise ValueError( "Cannot calculate P Model predictions for values below" " -25°C. See calc_density_h2o." ) # Guard against negative VPD issues - if np.nanmin(self.vpd) < 0: + if np.nanmin(self.vpd) < np.array([0]): raise ValueError( "Negative VPD values will lead to missing data - clip to " "zero or explicitly set to np.nan" @@ -309,25 +309,29 @@ class PModel: :func:`~pyrealm.pmodel.functions.calc_ftemp_kphio`). Examples: - >>> env = PModelEnvironment(tc=20, vpd=1000, co2=400, patm=101325.0) + >>> import numpy as np + >>> env = PModelEnvironment( + ... tc=np.array([20]), vpd=np.array([1000]), + ... co2=np.array([400]), patm=np.array([101325.0]) + ... ) + >>> # Predictions from C3 P model >>> mod_c3 = PModel(env) - >>> # Key variables from pmodel - >>> np.round(mod_c3.optchi.ci, 5) - 28.14209 - >>> np.round(mod_c3.optchi.chi, 5) - 0.69435 + >>> mod_c3.optchi.ci.round(5) + array([28.14209]) + >>> mod_c3.optchi.chi.round(5) + array([0.69435]) >>> mod_c3.estimate_productivity(fapar=1, ppfd=300) - >>> np.round(mod_c3.gpp, 5) - 76.42545 + >>> mod_c3.gpp.round(5) + array([76.42545]) + >>> # Predictions from C4 P model >>> mod_c4 = PModel(env, method_optchi='c4', method_jmaxlim='none') - >>> # Key variables from PModel - >>> np.round(mod_c4.optchi.ci, 5) - 18.22528 - >>> np.round(mod_c4.optchi.chi, 5) - 0.44967 + >>> mod_c4.optchi.ci.round(5) + array([18.22528]) + >>> mod_c4.optchi.chi.round(5) + array([0.44967]) >>> mod_c4.estimate_productivity(fapar=1, ppfd=300) - >>> np.round(mod_c4.gpp, 5) - 103.25886 + >>> mod_c4.gpp.round(5) + array([103.25886]) """ def __init__( @@ -796,16 +800,20 @@ def prentice14(self) -> None: assimilation. Examples: - >>> env = PModelEnvironment(tc= 20, patm=101325, co2=400, vpd=1000) + >>> import numpy as np + >>> env = PModelEnvironment( + ... tc=np.array([20]), vpd=np.array([1000]), + ... co2=np.array([400]), patm=np.array([101325.0]) + ... ) >>> vals = CalcOptimalChi(env=env) - >>> round(vals.chi, 5) - 0.69435 - >>> round(vals.mc, 5) - 0.33408 - >>> round(vals.mj, 5) - 0.7123 - >>> round(vals.mjoc, 5) - 2.13211 + >>> vals.chi.round(5) + array([0.69435]) + >>> vals.mc.round(5) + array([0.33408]) + >>> vals.mj.round(5) + array([0.7123]) + >>> vals.mjoc.round(5) + array([2.13211]) """ # TODO: Docstring - equation for m_j previously included term now @@ -854,19 +862,22 @@ def lavergne20_c3(self) -> None: `rootzonestress` approach. Examples: - >>> env = PModelEnvironment(tc=20, patm=101325, co2=400, - ... vpd=1000, theta=0.5) + >>> import numpy as np + >>> env = PModelEnvironment( + ... tc=np.array([20]), vpd=np.array([1000]), co2=np.array([400]), + ... patm=np.array([101325.0]), theta=np.array([0.5]) + ... ) >>> vals = CalcOptimalChi(env=env, method='lavergne20_c3') - >>> round(vals.beta, 5) - 224.75255 - >>> round(vals.chi, 5) - 0.73663 - >>> round(vals.mc, 5) - 0.34911 - >>> round(vals.mj, 5) - 0.7258 - >>> round(vals.mjoc, 5) - 2.07901 + >>> vals.beta.round(5) + array([224.75255]) + >>> vals.chi.round(5) + array([0.73663]) + >>> vals.mc.round(5) + array([0.34911]) + >>> vals.mj.round(5) + array([0.7258]) + >>> vals.mjoc.round(5) + array([2.07901]) """ # This method needs theta @@ -924,19 +935,22 @@ def lavergne20_c4(self) -> None: values and soil moisture in leaf gas exchange measurements. Examples: - >>> env = PModelEnvironment(tc=20, patm=101325, co2=400, - ... vpd=1000, theta=0.5) + >>> import numpy as np + >>> env = PModelEnvironment( + ... tc=np.array([20]), vpd=np.array([1000]), co2=np.array([400]), + ... patm=np.array([101325.0]), theta=np.array([0.5]) + ... ) >>> vals = CalcOptimalChi(env=env, method='lavergne20_c4') - >>> round(vals.beta, 5) - 24.97251 - >>> round(vals.chi, 5) - 0.44432 - >>> round(vals.mc, 5) - 0.28091 - >>> round(vals.mj, 5) - 1.0 - >>> round(vals.mjoc, 5) - 3.55989 + >>> vals.beta.round(5) + array([24.97251]) + >>> vals.chi.round(5) + array([0.44432]) + >>> vals.mc.round(5) + array([0.28091]) + >>> vals.mj.round(5) + array([1.]) + >>> vals.mjoc.round(5) + array([3.55989]) """ # Warn that this is experimental @@ -982,14 +996,18 @@ def c4(self) -> None: photosynthesis. Examples: - >>> env = PModelEnvironment(tc= 20, patm=101325, co2=400, vpd=1000) + >>> import numpy as np + >>> env = PModelEnvironment( + ... tc=np.array([20]), vpd=np.array([1000]), co2=np.array([400]), + ... patm=np.array([101325.0]), theta=np.array([0.5]) + ... ) >>> vals = CalcOptimalChi(env=env, method='c4') - >>> round(vals.chi, 5) - 0.44967 - >>> round(vals.mj, 1) - 1.0 - >>> round(vals.mc, 1) - 1.0 + >>> vals.chi.round(5) + array([0.44967]) + >>> vals.mj.round(1) + array([1.]) + >>> vals.mc.round(1) + array([1.]) """ # Replace missing rootzonestress with 1 @@ -1046,14 +1064,18 @@ def c4_no_gamma(self) -> None: \] Examples: - >>> env = PModelEnvironment(tc= 20, patm=101325, co2=400, vpd=1000) + >>> import numpy as np + >>> env = PModelEnvironment( + ... tc=np.array([20]), vpd=np.array([1000]), + ... co2=np.array([400]), patm=np.array([101325.0]) + ... ) >>> vals = CalcOptimalChi(env=env, method='c4_no_gamma') - >>> round(vals.chi, 5) - 0.3919 - >>> round(vals.mj, 1) - 1.0 - >>> round(vals.mc, 1) - 0.3 + >>> vals.chi.round(5) + array([0.3919]) + >>> vals.mj.round(1) + array([1.]) + >>> vals.mc.round(1) + array([0.3]) """ # Replace missing rootzonestress with 1 @@ -1127,23 +1149,27 @@ class JmaxLimitation: const: An instance of :class:`~pyrealm.constants.pmodel_const.PModelConst`. Examples: - >>> env = PModelEnvironment(tc= 20, patm=101325, co2=400, vpd=1000) + >>> import numpy as np + >>> env = PModelEnvironment( + ... tc=np.array([20]), vpd=np.array([1000]), + ... co2=np.array([400]), patm=np.array([101325.0]) + ... ) >>> optchi = CalcOptimalChi(env) >>> simple = JmaxLimitation(optchi, method='simple') >>> simple.f_j - 1.0 + array([1.]) >>> simple.f_v - 1.0 + array([1.]) >>> wang17 = JmaxLimitation(optchi, method='wang17') - >>> round(wang17.f_j, 5) - 0.66722 - >>> round(wang17.f_v, 5) - 0.55502 + >>> wang17.f_j.round(5) + array([0.66722]) + >>> wang17.f_v.round(5) + array([0.55502]) >>> smith19 = JmaxLimitation(optchi, method='smith19') - >>> round(smith19.f_j, 5) - 1.10204 - >>> round(smith19.f_v, 5) - 0.75442 + >>> smith19.f_j.round(5) + array([1.10204]) + >>> smith19.f_v.round(5) + array([0.75442]) """ # TODO - apparent incorrectness of wang and smith methods with _ca_ variation, From e28ad4f2565105dc3cdfb9dbb4a10693bf99c89d Mon Sep 17 00:00:00 2001 From: David Orme Date: Wed, 23 Aug 2023 10:38:10 +0100 Subject: [PATCH 24/39] Doctest fixes in pyrealm utilities --- pyrealm/utilities.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyrealm/utilities.py b/pyrealm/utilities.py index 2c1b6760..9cda24e2 100644 --- a/pyrealm/utilities.py +++ b/pyrealm/utilities.py @@ -70,7 +70,7 @@ def check_input_shapes(*args: Union[float, int, np.generic, np.ndarray, None]) - >>> check_input_shapes(np.array([1,2,3]), 5) (3,) >>> check_input_shapes(4, 5) - 1 + (1,) >>> check_input_shapes(np.array([1,2,3]), np.array([1,2])) Traceback (most recent call last): ... @@ -284,13 +284,13 @@ def bounds_mask( >>> vals = np.array([-15, 20, 30, 124], dtype=np.float) >>> np.nansum(vals) 159.0 - >>> vals_c = input_mask(vals, 0, 100, label='temperature') + >>> vals_c = bounds_mask(vals, 0, 100, label='temperature') >>> np.nansum(vals_c) 50.0 - >>> vals_c = input_mask(vals, 0, 124, interval_type='[]', label='temperature') + >>> vals_c = bounds_mask(vals, 0, 124, interval_type='[]', label='temperature') >>> np.nansum(vals_c) 174.0 - >>> vals_c = input_mask(vals, 0, 124, interval_type='[)', label='temperature') + >>> vals_c = bounds_mask(vals, 0, 124, interval_type='[)', label='temperature') >>> np.nansum(vals_c) 50.0 """ From d7223402dee95bd12a6eda2ef1d85a083876254f Mon Sep 17 00:00:00 2001 From: David Orme Date: Wed, 23 Aug 2023 10:45:46 +0100 Subject: [PATCH 25/39] Doctest fixes in hygro --- pyrealm/hygro.py | 52 ++++++++++++++++++++++++------------------------ 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/pyrealm/hygro.py b/pyrealm/hygro.py index 817d03ef..af24d552 100644 --- a/pyrealm/hygro.py +++ b/pyrealm/hygro.py @@ -37,15 +37,15 @@ def calc_vp_sat(ta: NDArray, const: HygroConst = HygroConst()) -> NDArray: >>> # Saturated vapour pressure at 21°C >>> import numpy as np >>> temp = np.array([21]) - >>> round(calc_vp_sat(temp), 6) - 2.480904 + >>> calc_vp_sat(temp).round(6) + array([2.480904]) >>> from pyrealm.constants import HygroConst >>> allen = HygroConst(magnus_option='Allen1998') - >>> round(calc_vp_sat(temp, const=allen), 6) - 2.487005 + >>> calc_vp_sat(temp, const=allen).round(6) + array([2.487005]) >>> alduchov = HygroConst(magnus_option='Alduchov1996') - >>> round(calc_vp_sat(temp, const=alduchov), 6) - 2.481888 + >>> calc_vp_sat(temp, const=alduchov).round(6) + array([2.481888]) """ # Magnus equation and conversion to kPa @@ -71,14 +71,14 @@ def convert_vp_to_vpd( Examples: >>> import numpy as np + >>> from pyrealm.constants import HygroConst >>> vp = np.array([1.9]) >>> temp = np.array([21]) - >>> round(convert_vp_to_vpd(vp, temp), 7) - 0.5809042 - >>> from pyrealm.constants import HygroConst + >>> convert_vp_to_vpd(vp, temp).round(7) + array([0.5809042]) >>> allen = HygroConst(magnus_option='Allen1998') - >>> round(convert_vp_to_vpd(vp, temp, const=allen), 7) - 0.5870054 + >>> convert_vp_to_vpd(vp, temp, const=allen).round(7) + array([0.5870054]) """ vp_sat = calc_vp_sat(ta, const=const) @@ -101,19 +101,19 @@ def convert_rh_to_vpd( Examples: >>> import numpy as np + >>> from pyrealm.constants import HygroConst + >>> import sys; sys.stderr = sys.stdout >>> rh = np.array([0.7]) >>> temp = np.array([21]) - >>> round(convert_rh_to_vpd(rh, temp), 7) - 0.7442712 - >>> from pyrealm.constants import HygroConst + >>> convert_rh_to_vpd(rh, temp).round(7) + array([0.7442712]) >>> allen = HygroConst(magnus_option='Allen1998') - >>> round(convert_rh_to_vpd(rh, temp, hygro_params=allen), 7) - 0.7461016 - >>> import sys; sys.stderr = sys.stdout + >>> convert_rh_to_vpd(rh, temp, const=allen).round(7) + array([0.7461016]) >>> rh_percent = np.array([70]) - >>> round(convert_rh_to_vpd(rh_percent, temp), 7) #doctest: +ELLIPSIS + >>> convert_rh_to_vpd(rh_percent, temp).round(7) #doctest: +ELLIPSIS pyrealm... contains values outside the expected range (0,1). Check units? - -171.1823864 + array([-171.1823864]) """ rh = bounds_checker(rh, 0, 1, "[]", "rh", "proportion") @@ -141,8 +141,8 @@ def convert_sh_to_vp( >>> import numpy as np >>> sh = np.array([0.006]) >>> patm = np.array([99.024]) - >>> round(convert_sh_to_vp(sh, patm), 7) - 0.9517451 + >>> convert_sh_to_vp(sh, patm).round(7) + array([0.9517451]) """ return sh * patm / ((1.0 - const.mwr) * sh + const.mwr) @@ -165,15 +165,15 @@ def convert_sh_to_vpd( Examples: >>> import numpy as np + >>> from pyrealm.constants import HygroConst >>> sh = np.array([0.006]) >>> temp = np.array([21]) >>> patm = np.array([99.024]) - >>> round(convert_sh_to_vpd(sh, temp, patm), 6) - 1.529159 - >>> from pyrealm.constants import HygroConst + >>> convert_sh_to_vpd(sh, temp, patm).round(6) + array([1.529159]) >>> allen = HygroConst(magnus_option='Allen1998') - >>> round(convert_sh_to_vpd(sh, temp, patm, hygro_params=allen), 5) - 1.53526 + >>> convert_sh_to_vpd(sh, temp, patm, const=allen).round(5) + array([1.53526]) """ vp_sat = calc_vp_sat(ta, const=const) From b80e57b17c1ec69cb49c738d15214a04d0f501f7 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 29 Aug 2023 14:59:54 +0100 Subject: [PATCH 26/39] Added example to PModelEnvironment docstring --- pyrealm/pmodel/pmodel.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/pyrealm/pmodel/pmodel.py b/pyrealm/pmodel/pmodel.py index 083dbf08..edc5ca5d 100644 --- a/pyrealm/pmodel/pmodel.py +++ b/pyrealm/pmodel/pmodel.py @@ -85,6 +85,13 @@ class PModelEnvironment: theta: Volumetric soil moisture (m3/m3) const: An instance of :class:`~pyrealm.constants.pmodel_const.PModelConst`. + + Examples: + >>> import numpy as np + >>> env = PModelEnvironment( + ... tc=np.array([20]), vpd=np.array([1000]), + ... co2=np.array([400]), patm=np.array([101325.0]) + ... ) """ def __init__( From 887a722f2cf0f18b8e505e8e51dd6079fdb09a70 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 29 Aug 2023 15:14:50 +0100 Subject: [PATCH 27/39] Added simple example to README --- README.md | 33 +++++++++++++++++++++++++++++---- 1 file changed, 29 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 0d4a50e9..8f8e42ce 100644 --- a/README.md +++ b/README.md @@ -30,10 +30,30 @@ The `pyrealm` package requires Python 3.9 or greater and can be installed from pip install pyrealm ``` -At present, the package is designed for use with Python scripts or Jupyter notebooks. -Users will typically load data, using for example [`numpy`](https://numpy.org/) or -[`xarray`](https://docs.xarray.dev/en/stable/), and then import and call `pyrealm` -classes and functions. +You can now get started using `pyrealm`. For example, to calculate the estimated gross +primary productivity of a C3 plant in a location, start a Python interpreter, using +`python`, `python3` or `ipython` depending on your installation, and run: + +```python +import numpy as np +from pyrealm.pmodel import PModelEnvironment, PModel + +# Calculate the photosynthetic environment given the conditions +env = PModelEnvironment( + tc=np.array([20]), vpd=np.array([1000]), + co2=np.array([400]), patm=np.array([101325.0]) +) + +# Calculate the predictions of the P Model for a C3 plant +pmodel_c3 = PModel(env) + +# Estimate the GPP from the model given the absorbed photosynthetically active light +pmodel_c3.estimate_productivity(fapar=1, ppfd=300) + +# Report the GPP in micrograms of carbon per m2 per second. +pmodel_c3.gpp +array([76.42544948]) +``` The package website provides worked examples of using `pyrealm`, for example to: @@ -45,6 +65,11 @@ The package website provides worked examples of using `pyrealm`, for example to: * [estimate C3/C4 competition](https://pyrealm.readthedocs.io/en/latest/users/pmodel/c3c4model.html#worked-example). +These worked examples also show how `pyrealm` can be used within Python scripts or +Jupyter notebooks and how to use `pyrealm` with large datasets loaded using +[`numpy`](https://numpy.org/) or [`xarray`](https://docs.xarray.dev/en/stable/) with +`pyrealm` classes and functions. + ## Developing `pyrealm` If you are interested in contributing to the development of `pyrealm`, please read the From fbaa8c309498a9af1265dbf924af3744cc991194 Mon Sep 17 00:00:00 2001 From: David Orme Date: Fri, 1 Sep 2023 09:52:15 +0100 Subject: [PATCH 28/39] Separate input from output in minimal example --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 8f8e42ce..fbf03f3e 100644 --- a/README.md +++ b/README.md @@ -52,6 +52,11 @@ pmodel_c3.estimate_productivity(fapar=1, ppfd=300) # Report the GPP in micrograms of carbon per m2 per second. pmodel_c3.gpp +``` + +This should give the following output: + +```python array([76.42544948]) ``` From 5e79bbb6bdbd4d563be1f40b05100db1e744d1e8 Mon Sep 17 00:00:00 2001 From: davidorme Date: Mon, 4 Sep 2023 00:04:39 +0000 Subject: [PATCH 29/39] chore: update pre-commit hooks --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index de1b92c9..8691e9f8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -24,7 +24,7 @@ repos: - id: mypy additional_dependencies: [numpy, types-tabulate] - repo: https://github.com/igorshubovych/markdownlint-cli - rev: v0.35.0 + rev: v0.36.0 hooks: - id: markdownlint From d9a77c9c8bd96652a21fe41660e7ce0455222f51 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 5 Sep 2023 20:07:38 +0100 Subject: [PATCH 30/39] Typed competition consts --- pyrealm/constants/competition_const.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/pyrealm/constants/competition_const.py b/pyrealm/constants/competition_const.py index b04963ca..5a14f650 100644 --- a/pyrealm/constants/competition_const.py +++ b/pyrealm/constants/competition_const.py @@ -15,17 +15,17 @@ class C3C4Const(ConstantsClass): # Non-linear regression of fraction C4 plants from proportion GPP advantage # of C4 over C3 plants - adv_to_frac_k = 6.63 + adv_to_frac_k: float = 6.63 """Coefficient k of C4 fraction estimation""" - adv_to_frac_q = 0.16 + adv_to_frac_q: float = 0.16 """Coefficient 1 of C4 fraction estimation""" # Conversion parameters to estimate tree cover from C3 GPP - gpp_to_tc_a = 15.60 + gpp_to_tc_a: float = 15.60 """Coefficient a of tree cover estimation""" - gpp_to_tc_b = 1.41 + gpp_to_tc_b: float = 1.41 """Coefficient b of tree cover estimation""" - gpp_to_tc_c = -7.72 + gpp_to_tc_c: float = -7.72 """Coefficient c of tree cover estimation""" - c3_forest_closure_gpp = 2.8 + c3_forest_closure_gpp: float = 2.8 """GPP at which forest canopy closure occurs""" From 6c540592a6bad8f20bd8d66f508d5dc76ba07628 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 5 Sep 2023 20:08:26 +0100 Subject: [PATCH 31/39] Using default_factory for mutable defaults in constants dataclasses --- pyrealm/constants/hygro_const.py | 6 ++- pyrealm/constants/pmodel_const.py | 84 +++++++++++++++++++------------ 2 files changed, 55 insertions(+), 35 deletions(-) diff --git a/pyrealm/constants/hygro_const.py b/pyrealm/constants/hygro_const.py index 728a19f3..652c4259 100644 --- a/pyrealm/constants/hygro_const.py +++ b/pyrealm/constants/hygro_const.py @@ -2,7 +2,7 @@ used in the hygrometer conversion functions in the :mod:`~pyrealm.hygro` module. """ # noqa: D205, D415 -from dataclasses import dataclass +from dataclasses import dataclass, field from typing import Optional import numpy as np @@ -23,7 +23,9 @@ class HygroConst(ConstantsClass): setting is to use the ``Sonntag1990`` parameters. """ - magnus_coef: NDArray[np.float32] = np.array((611.2, 17.62, 243.12)) + magnus_coef: NDArray[np.float32] = field( + default_factory=lambda: np.array((611.2, 17.62, 243.12)) + ) """Three coefficients of the Magnus equation for saturated vapour pressure.""" mwr: float = 0.622 """The ratio molecular weight of water vapour to dry air (:math:`MW_r`, -)""" diff --git a/pyrealm/constants/pmodel_const.py b/pyrealm/constants/pmodel_const.py index 51f96457..dcfc6b89 100644 --- a/pyrealm/constants/pmodel_const.py +++ b/pyrealm/constants/pmodel_const.py @@ -1,6 +1,6 @@ """The pmodel_const module TODO.""" -from dataclasses import dataclass +from dataclasses import dataclass, field import numpy as np from numpy.typing import NDArray @@ -125,31 +125,37 @@ class PModelConst(ConstantsClass): """Conversion from °C to K (:math:`CtoK` , 273.15, -)""" # Fisher Dial - fisher_dial_lambda: NDArray[np.float32] = np.array( - [1788.316, 21.55053, -0.4695911, 0.003096363, -7.341182e-06] + fisher_dial_lambda: NDArray[np.float32] = field( + default_factory=lambda: np.array( + [1788.316, 21.55053, -0.4695911, 0.003096363, -7.341182e-06] + ) ) r"""Temperature dependent lambda parameterisation of the Tumlirz equation. (:math:`\lambda`).""" - fisher_dial_Po: NDArray[np.float32] = np.array( - [5918.499, 58.05267, -1.1253317, 0.0066123869, -1.4661625e-05] + fisher_dial_Po: NDArray[np.float32] = field( + default_factory=lambda: np.array( + [5918.499, 58.05267, -1.1253317, 0.0066123869, -1.4661625e-05] + ) ) """Temperature dependent P0 parameterisation of the Tumlirz equation (:math:`P_0`).""" - fisher_dial_Vinf: NDArray[np.float32] = np.array( - [ - 0.6980547, - -0.0007435626, - 3.704258e-05, - -6.315724e-07, - 9.829576e-09, - -1.197269e-10, - 1.005461e-12, - -5.437898e-15, - 1.69946e-17, - -2.295063e-20, - ] + fisher_dial_Vinf: NDArray[np.float32] = field( + default_factory=lambda: np.array( + [ + 0.6980547, + -0.0007435626, + 3.704258e-05, + -6.315724e-07, + 9.829576e-09, + -1.197269e-10, + 1.005461e-12, + -5.437898e-15, + 1.69946e-17, + -2.295063e-20, + ] + ) ) r"""Temperature dependent Vinf parameterisation of the Tumlirz equation (:math:`V_{\infty}`).""" @@ -164,18 +170,22 @@ class PModelConst(ConstantsClass): huber_mu_ast: float = 1e-06 r"""Huber reference pressure (:math:`\mu_{ast}` 1.0e-6, Pa s)""" - huber_H_i: NDArray[np.float32] = np.array([1.67752, 2.20462, 0.6366564, -0.241605]) + huber_H_i: NDArray[np.float32] = field( + default_factory=lambda: np.array([1.67752, 2.20462, 0.6366564, -0.241605]) + ) """Temperature dependent parameterisation of Hi in Huber.""" - huber_H_ij: NDArray[np.float32] = np.array( - [ - [0.520094, 0.0850895, -1.08374, -0.289555, 0.0, 0.0], - [0.222531, 0.999115, 1.88797, 1.26613, 0.0, 0.120573], - [-0.281378, -0.906851, -0.772479, -0.489837, -0.25704, 0.0], - [0.161913, 0.257399, 0.0, 0.0, 0.0, 0.0], - [-0.0325372, 0.0, 0.0, 0.0698452, 0.0, 0.0], - [0.0, 0.0, 0.0, 0.0, 0.00872102, 0.0], - [0.0, 0.0, 0.0, -0.00435673, 0.0, -0.000593264], - ], + huber_H_ij: NDArray[np.float32] = field( + default_factory=lambda: np.array( + [ + [0.520094, 0.0850895, -1.08374, -0.289555, 0.0, 0.0], + [0.222531, 0.999115, 1.88797, 1.26613, 0.0, 0.120573], + [-0.281378, -0.906851, -0.772479, -0.489837, -0.25704, 0.0], + [0.161913, 0.257399, 0.0, 0.0, 0.0, 0.0], + [-0.0325372, 0.0, 0.0, 0.0698452, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.00872102, 0.0], + [0.0, 0.0, 0.0, -0.00435673, 0.0, -0.000593264], + ], + ) ) """Temperature and mass density dependent parameterisation of Hij in Huber.""" @@ -201,9 +211,13 @@ class PModelConst(ConstantsClass): # - note that kphio_C4 has been updated to account for an unintended double # 8 fold downscaling to account for the fraction of light reaching PS2. # from original values of [-0.008, 0.00375, -0.58e-4] - kphio_C4: NDArray[np.float32] = np.array((-0.064, 0.03, -0.000464)) + kphio_C4: NDArray[np.float32] = field( + default_factory=lambda: np.array((-0.064, 0.03, -0.000464)) + ) """Quadratic scaling of Kphio with temperature for C4 plants""" - kphio_C3: NDArray[np.float32] = np.array((0.352, 0.022, -0.00034)) + kphio_C3: NDArray[np.float32] = field( + default_factory=lambda: np.array((0.352, 0.022, -0.00034)) + ) """Quadratic scaling of Kphio with temperature for C3 plants""" # Bernachhi @@ -251,9 +265,13 @@ class PModelConst(ConstantsClass): """Exponent of the threshold function for Mengoli soil moisture""" # Unit cost ratio (beta) values for different CalcOptimalChi methods - beta_cost_ratio_prentice14: NDArray[np.float32] = np.array([146.0]) + beta_cost_ratio_prentice14: NDArray[np.float32] = field( + default_factory=lambda: np.array([146.0]) + ) r"""Unit cost ratio for C3 plants (:math:`\beta`, 146.0).""" - beta_cost_ratio_c4: NDArray[np.float32] = np.array([146.0 / 9]) + beta_cost_ratio_c4: NDArray[np.float32] = field( + default_factory=lambda: np.array([146.0 / 9]) + ) r"""Unit cost ratio for C4 plants (:math:`\beta`, 16.222).""" lavergne_2020_b_c3: float = 1.73 """Slope of soil moisture effects on beta for C3 plants""" From 238022e5649907001fd216e98f82db2775b51f43 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 5 Sep 2023 20:08:51 +0100 Subject: [PATCH 32/39] Deprecated use of np.float in docstrings --- pyrealm/utilities.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyrealm/utilities.py b/pyrealm/utilities.py index 9cda24e2..27c870c9 100644 --- a/pyrealm/utilities.py +++ b/pyrealm/utilities.py @@ -236,7 +236,7 @@ def bounds_checker( The function returns the contents of values. Examples: - >>> vals = np.array([-15, 20, 30, 124], dtype=np.float) + >>> vals = np.array([-15, 20, 30, 124], dtype=float) >>> vals_c = bounds_checker(vals, 0, 100, label='temperature', unit='°C') """ @@ -281,7 +281,7 @@ def bounds_mask( a float np.ndarray object with out of bounds values replaced with np.nan. Examples: - >>> vals = np.array([-15, 20, 30, 124], dtype=np.float) + >>> vals = np.array([-15, 20, 30, 124], dtype=float) >>> np.nansum(vals) 159.0 >>> vals_c = bounds_mask(vals, 0, 100, label='temperature') From e4b8174ab5574acafc43773e1bcf67e706a3c105 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 5 Sep 2023 20:09:56 +0100 Subject: [PATCH 33/39] Updated pyproject and poetry.lock to add Python 3.11 --- poetry.lock | 2614 ++++++++++++++++++++++++++---------------------- pyproject.toml | 2 +- 2 files changed, 1442 insertions(+), 1174 deletions(-) diff --git a/poetry.lock b/poetry.lock index c85f634b..23b604c1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,10 @@ [[package]] name = "alabaster" -version = "0.7.12" +version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.6" [[package]] name = "appnope" @@ -16,53 +16,51 @@ python-versions = "*" [[package]] name = "asttokens" -version = "2.2.1" +version = "2.4.0" description = "Annotate AST trees with source code positions" category = "dev" optional = false python-versions = "*" [package.dependencies] -six = "*" +six = ">=1.12.0" [package.extras] test = ["astroid", "pytest"] [[package]] name = "attrs" -version = "22.1.0" +version = "23.1.0" description = "Classes Without Boilerplate" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.7" [package.extras] -dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"] -docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] -tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "zope.interface"] -tests-no-zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy (>=0.900,!=0.940)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins"] +cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] +dev = ["attrs[docs,tests]", "pre-commit"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"] +tests = ["attrs[tests-no-zope]", "zope-interface"] +tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"] [[package]] name = "autodocsumm" -version = "0.2.9" +version = "0.2.11" description = "Extended sphinx autodoc including automatic autosummaries" category = "dev" optional = false python-versions = ">=3.7" [package.dependencies] -Sphinx = ">=2.2,<6.0" +Sphinx = ">=2.2,<8.0" [[package]] name = "babel" -version = "2.11.0" +version = "2.12.1" description = "Internationalization utilities" category = "dev" optional = false -python-versions = ">=3.6" - -[package.dependencies] -pytz = ">=2015.7" +python-versions = ">=3.7" [[package]] name = "backcall" @@ -96,7 +94,7 @@ uvloop = ["uvloop (>=0.15.2)"] [[package]] name = "bottleneck" -version = "1.3.5" +version = "1.3.7" description = "Fast NumPy array functions written in C" category = "main" optional = false @@ -110,7 +108,7 @@ doc = ["gitpython", "numpydoc", "sphinx"] [[package]] name = "certifi" -version = "2022.12.7" +version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." category = "dev" optional = false @@ -129,11 +127,11 @@ pycparser = "*" [[package]] name = "cfgv" -version = "3.3.1" +version = "3.4.0" description = "Validate configuration and produce human readable error messages." category = "dev" optional = false -python-versions = ">=3.6.1" +python-versions = ">=3.8" [[package]] name = "cftime" @@ -148,18 +146,15 @@ numpy = ">1.13.3" [[package]] name = "charset-normalizer" -version = "2.1.1" +version = "3.2.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "dev" optional = false -python-versions = ">=3.6.0" - -[package.extras] -unicode-backport = ["unicodedata2"] +python-versions = ">=3.7.0" [[package]] name = "click" -version = "8.1.3" +version = "8.1.7" description = "Composable command line interface toolkit" category = "dev" optional = false @@ -178,43 +173,45 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7 [[package]] name = "comm" -version = "0.1.2" +version = "0.1.4" description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." category = "dev" optional = false python-versions = ">=3.6" [package.dependencies] -traitlets = ">=5.3" +traitlets = ">=4" [package.extras] +lint = ["black (>=22.6.0)", "mdformat (>0.7)", "mdformat-gfm (>=0.3.5)", "ruff (>=0.0.156)"] test = ["pytest"] +typing = ["mypy (>=0.990)"] [[package]] name = "contourpy" -version = "1.0.6" +version = "1.1.0" description = "Python library for calculating contours of 2D quadrilateral grids" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] numpy = ">=1.16" [package.extras] bokeh = ["bokeh", "selenium"] -docs = ["docutils (<0.18)", "sphinx (<=5.2.0)", "sphinx-rtd-theme"] -test = ["Pillow", "flake8", "isort", "matplotlib", "pytest"] -test-minimal = ["pytest"] -test-no-codebase = ["Pillow", "matplotlib", "pytest"] +docs = ["furo", "sphinx-copybutton"] +mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.2.0)", "types-Pillow"] +test = ["Pillow", "contourpy[test-no-images]", "matplotlib"] +test-no-images = ["pytest", "pytest-cov", "wurlitzer"] [[package]] name = "coverage" -version = "6.5.0" +version = "7.3.0" description = "Code coverage measurement for Python" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""} @@ -232,18 +229,18 @@ python-versions = ">=3.6" [[package]] name = "dacite" -version = "1.6.0" +version = "1.8.1" description = "Simple creation of data classes from dictionaries." category = "main" optional = false python-versions = ">=3.6" [package.extras] -dev = ["black", "coveralls", "mypy", "pylint", "pytest (>=5)", "pytest-cov"] +dev = ["black", "coveralls", "mypy", "pre-commit", "pylint", "pytest (>=5)", "pytest-benchmark", "pytest-cov"] [[package]] name = "debugpy" -version = "1.6.4" +version = "1.6.7.post1" description = "An implementation of the Debug Adapter Protocol for Python" category = "dev" optional = false @@ -259,7 +256,7 @@ python-versions = ">=3.5" [[package]] name = "distlib" -version = "0.3.6" +version = "0.3.7" description = "Distribution utilities" category = "dev" optional = false @@ -273,17 +270,9 @@ category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -[[package]] -name = "entrypoints" -version = "0.4" -description = "Discover and load entry points from installed packages." -category = "dev" -optional = false -python-versions = ">=3.6" - [[package]] name = "exceptiongroup" -version = "1.0.4" +version = "1.1.3" description = "Backport of PEP 654 (exception groups)" category = "dev" optional = false @@ -305,7 +294,7 @@ tests = ["asttokens", "littleutils", "pytest", "rich"] [[package]] name = "fastjsonschema" -version = "2.16.2" +version = "2.18.0" description = "Fastest Python implementation of JSON schema" category = "dev" optional = false @@ -316,15 +305,18 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc [[package]] name = "filelock" -version = "3.8.2" +version = "3.12.3" description = "A platform independent file lock." category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" + +[package.dependencies] +typing-extensions = {version = ">=4.7.1", markers = "python_version < \"3.11\""} [package.extras] -docs = ["furo (>=2022.9.29)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"] -testing = ["covdefaults (>=2.2.2)", "coverage (>=6.5)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"] +docs = ["furo (>=2023.7.26)", "sphinx (>=7.1.2)", "sphinx-autodoc-typehints (>=1.24)"] +testing = ["covdefaults (>=2.3)", "coverage (>=7.3)", "diff-cover (>=7.7)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-timeout (>=2.1)"] [[package]] name = "flake8" @@ -341,11 +333,11 @@ pyflakes = ">=2.4.0,<2.5.0" [[package]] name = "flake8-docstrings" -version = "1.6.0" +version = "1.7.0" description = "Extension for flake8 which uses pydocstyle to check docstrings" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.7" [package.dependencies] flake8 = ">=3" @@ -353,14 +345,14 @@ pydocstyle = ">=2.1" [[package]] name = "fonttools" -version = "4.38.0" +version = "4.42.1" description = "Tools to manipulate font files" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] -all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"] +all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=15.0.0)", "xattr", "zopfli (>=0.1.4)"] graphite = ["lz4 (>=1.7.4.2)"] interpolatable = ["munkres", "scipy"] lxml = ["lxml (>=4.0,<5)"] @@ -370,12 +362,12 @@ repacker = ["uharfbuzz (>=0.23.0)"] symfont = ["sympy"] type1 = ["xattr"] ufo = ["fs (>=2.2.0,<3)"] -unicode = ["unicodedata2 (>=14.0.0)"] +unicode = ["unicodedata2 (>=15.0.0)"] woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"] [[package]] name = "greenlet" -version = "2.0.1" +version = "2.0.2" description = "Lightweight in-process concurrent programming" category = "dev" optional = false @@ -383,15 +375,15 @@ python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" [package.extras] docs = ["Sphinx", "docutils (<0.18)"] -test = ["faulthandler", "objgraph", "psutil"] +test = ["objgraph", "psutil"] [[package]] name = "identify" -version = "2.5.9" +version = "2.5.27" description = "File identification library for Python" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] license = ["ukkonen"] @@ -414,31 +406,46 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "5.1.0" +version = "6.8.0" description = "Read metadata from Python packages" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] zipp = ">=0.5" [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] perf = ["ipython"] -testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)"] +testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"] + +[[package]] +name = "importlib-resources" +version = "6.0.1" +description = "Read resources from Python packages" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""} + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [[package]] name = "iniconfig" -version = "1.1.1" -description = "iniconfig: brain-dead simple config-ini parsing" +version = "2.0.0" +description = "brain-dead simple config-ini parsing" category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.7" [[package]] name = "ipykernel" -version = "6.19.2" +version = "6.25.2" description = "IPython Kernel for Jupyter" category = "dev" optional = false @@ -447,50 +454,53 @@ python-versions = ">=3.8" [package.dependencies] appnope = {version = "*", markers = "platform_system == \"Darwin\""} comm = ">=0.1.1" -debugpy = ">=1.0" +debugpy = ">=1.6.5" ipython = ">=7.23.1" jupyter-client = ">=6.1.12" +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" matplotlib-inline = ">=0.1" nest-asyncio = "*" packaging = "*" psutil = "*" -pyzmq = ">=17" +pyzmq = ">=20" tornado = ">=6.1" traitlets = ">=5.4.0" [package.extras] cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"] -docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt"] -lint = ["black (>=22.6.0)", "mdformat (>0.7)", "ruff (>=0.0.156)"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"] +pyqt5 = ["pyqt5"] +pyside6 = ["pyside6"] test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov", "pytest-timeout"] -typing = ["mypy (>=0.990)"] [[package]] name = "ipython" -version = "8.9.0" +version = "8.15.0" description = "IPython: Productive Interactive Computing" category = "dev" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" [package.dependencies] appnope = {version = "*", markers = "sys_platform == \"darwin\""} backcall = "*" colorama = {version = "*", markers = "sys_platform == \"win32\""} decorator = "*" +exceptiongroup = {version = "*", markers = "python_version < \"3.11\""} jedi = ">=0.16" matplotlib-inline = "*" pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""} pickleshare = "*" -prompt-toolkit = ">=3.0.30,<3.1.0" +prompt-toolkit = ">=3.0.30,<3.0.37 || >3.0.37,<3.1.0" pygments = ">=2.4.0" stack-data = "*" traitlets = ">=5" +typing-extensions = {version = "*", markers = "python_version < \"3.10\""} [package.extras] -all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.20)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"] +all = ["black", "curio", "docrepr", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.21)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"] black = ["black"] -doc = ["docrepr", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"] +doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"] kernel = ["ipykernel"] nbconvert = ["nbconvert"] nbformat = ["nbformat"] @@ -498,7 +508,7 @@ notebook = ["ipywidgets", "notebook"] parallel = ["ipyparallel"] qtconsole = ["qtconsole"] test = ["pytest (<7.1)", "pytest-asyncio", "testpath"] -test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.20)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"] +test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.21)", "pandas", "pytest (<7.1)", "pytest-asyncio", "testpath", "trio"] [[package]] name = "isort" @@ -516,18 +526,18 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] [[package]] name = "jedi" -version = "0.18.2" +version = "0.19.0" description = "An autocompletion tool for Python that can be used for text editors." category = "dev" optional = false python-versions = ">=3.6" [package.dependencies] -parso = ">=0.8.0,<0.9.0" +parso = ">=0.8.3,<0.9.0" [package.extras] docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"] -qa = ["flake8 (==3.8.3)", "mypy (==0.782)"] +qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"] testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"] [[package]] @@ -546,20 +556,33 @@ i18n = ["Babel (>=2.7)"] [[package]] name = "jsonschema" -version = "4.17.3" +version = "4.19.0" description = "An implementation of JSON Schema validation for Python" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] -attrs = ">=17.4.0" -pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2" +attrs = ">=22.2.0" +jsonschema-specifications = ">=2023.03.6" +referencing = ">=0.28.4" +rpds-py = ">=0.7.1" [package.extras] format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"] +[[package]] +name = "jsonschema-specifications" +version = "2023.7.1" +description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +referencing = ">=0.28.0" + [[package]] name = "jupyter-cache" version = "0.5.0" @@ -586,28 +609,27 @@ testing = ["coverage", "ipykernel", "jupytext", "matplotlib", "nbdime", "nbforma [[package]] name = "jupyter-client" -version = "7.4.8" +version = "8.3.1" description = "Jupyter protocol implementation and client libraries" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] -entrypoints = "*" -jupyter-core = ">=4.9.2" -nest-asyncio = ">=1.5.4" +importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""} +jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" python-dateutil = ">=2.8.2" pyzmq = ">=23.0" tornado = ">=6.2" -traitlets = "*" +traitlets = ">=5.3" [package.extras] -doc = ["ipykernel", "myst-parser", "sphinx (>=1.3.6)", "sphinx-rtd-theme", "sphinxcontrib-github-alt"] -test = ["codecov", "coverage", "ipykernel (>=6.12)", "ipython", "mypy", "pre-commit", "pytest", "pytest-asyncio (>=0.18)", "pytest-cov", "pytest-timeout"] +docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] +test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"] [[package]] name = "jupyter-core" -version = "5.1.0" +version = "5.3.1" description = "Jupyter core package. A base package on which Jupyter projects rely." category = "dev" optional = false @@ -615,16 +637,16 @@ python-versions = ">=3.8" [package.dependencies] platformdirs = ">=2.5" -pywin32 = {version = ">=1.0", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} +pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""} traitlets = ">=5.3" [package.extras] -docs = ["myst-parser", "sphinxcontrib-github-alt", "traitlets"] +docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"] test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"] [[package]] name = "kiwisolver" -version = "1.4.4" +version = "1.4.5" description = "A fast implementation of the Cassowary constraint solver" category = "dev" optional = false @@ -643,7 +665,7 @@ six = ">=1.4.1" [[package]] name = "markdown-it-py" -version = "2.1.0" +version = "2.2.0" description = "Python port of markdown-it. Markdown parsing, done right!" category = "dev" optional = false @@ -653,10 +675,10 @@ python-versions = ">=3.7" mdurl = ">=0.1,<1.0" [package.extras] -benchmarking = ["psutil", "pytest", "pytest-benchmark (>=3.2,<4.0)"] -code-style = ["pre-commit (==2.6)"] -compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.3.6,<3.4.0)", "mistletoe (>=0.8.1,<0.9.0)", "mistune (>=2.0.2,<2.1.0)", "panflute (>=2.1.3,<2.2.0)"] -linkify = ["linkify-it-py (>=1.0,<2.0)"] +benchmarking = ["psutil", "pytest", "pytest-benchmark"] +code-style = ["pre-commit (>=3.0,<4.0)"] +compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"] +linkify = ["linkify-it-py (>=1,<3)"] plugins = ["mdit-py-plugins"] profiling = ["gprof2dot"] rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"] @@ -664,7 +686,7 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] [[package]] name = "markupsafe" -version = "2.1.1" +version = "2.1.3" description = "Safely add untrusted strings to HTML/XML markup." category = "dev" optional = false @@ -672,7 +694,7 @@ python-versions = ">=3.7" [[package]] name = "matplotlib" -version = "3.6.2" +version = "3.7.2" description = "Python plotting package" category = "dev" optional = false @@ -682,11 +704,12 @@ python-versions = ">=3.8" contourpy = ">=1.0.1" cycler = ">=0.10" fonttools = ">=4.22.0" +importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""} kiwisolver = ">=1.0.1" -numpy = ">=1.19" +numpy = ">=1.20" packaging = ">=20.0" pillow = ">=6.2.0" -pyparsing = ">=2.2.1" +pyparsing = ">=2.3.1,<3.1" python-dateutil = ">=2.7" setuptools_scm = ">=7" @@ -711,7 +734,7 @@ python-versions = "*" [[package]] name = "mdit-py-plugins" -version = "0.3.3" +version = "0.3.5" description = "Collection of plugins for markdown-it-py" category = "dev" optional = false @@ -754,11 +777,11 @@ reports = ["lxml"] [[package]] name = "mypy-extensions" -version = "0.4.3" -description = "Experimental type system extensions for programs checked with the mypy typechecker." +version = "1.0.0" +description = "Type system extensions for programs checked with the mypy type checker." category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.5" [[package]] name = "myst-nb" @@ -829,11 +852,11 @@ test = ["black", "check-manifest", "flake8", "ipykernel", "ipython (<8.0.0)", "i [[package]] name = "nbformat" -version = "5.7.0" +version = "5.9.2" description = "The Jupyter Notebook format" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.dependencies] fastjsonschema = "*" @@ -842,11 +865,12 @@ jupyter-core = "*" traitlets = ">=5.1" [package.extras] -test = ["check-manifest", "pep440", "pre-commit", "pytest", "testpath"] +docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"] +test = ["pep440", "pre-commit", "pytest", "testpath"] [[package]] name = "nest-asyncio" -version = "1.5.6" +version = "1.5.7" description = "Patch asyncio to allow nested event loops" category = "dev" optional = false @@ -854,19 +878,20 @@ python-versions = ">=3.5" [[package]] name = "netcdf4" -version = "1.6.3" +version = "1.6.4" description = "Provides an object-oriented python interface to the netCDF version 4 library" category = "dev" optional = false python-versions = ">=3.7" [package.dependencies] +certifi = "*" cftime = "*" numpy = "*" [[package]] name = "nodeenv" -version = "1.7.0" +version = "1.8.0" description = "Node.js virtual environment builder" category = "dev" optional = false @@ -877,15 +902,15 @@ setuptools = "*" [[package]] name = "numpy" -version = "1.23.5" -description = "NumPy is the fundamental package for array computing with Python." +version = "1.25.2" +description = "Fundamental package for array computing in Python" category = "main" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" [[package]] name = "packaging" -version = "22.0" +version = "23.1" description = "Core utilities for Python packages" category = "dev" optional = false @@ -893,43 +918,44 @@ python-versions = ">=3.7" [[package]] name = "pandas" -version = "2.0.0" +version = "2.1.0" description = "Powerful data structures for data analysis, time series, and statistics" category = "dev" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" [package.dependencies] numpy = [ - {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, - {version = ">=1.20.3", markers = "python_version < \"3.10\""}, + {version = ">=1.22.4", markers = "python_version < \"3.11\""}, + {version = ">=1.23.2", markers = "python_version >= \"3.11\""}, ] python-dateutil = ">=2.8.2" pytz = ">=2020.1" tzdata = ">=2022.1" [package.extras] -all = ["PyQt5 (>=5.15.1)", "SQLAlchemy (>=1.4.16)", "beautifulsoup4 (>=4.9.3)", "bottleneck (>=1.3.2)", "brotlipy (>=0.7.0)", "fastparquet (>=0.6.3)", "fsspec (>=2021.07.0)", "gcsfs (>=2021.07.0)", "html5lib (>=1.1)", "hypothesis (>=6.34.2)", "jinja2 (>=3.0.0)", "lxml (>=4.6.3)", "matplotlib (>=3.6.1)", "numba (>=0.53.1)", "numexpr (>=2.7.3)", "odfpy (>=1.4.1)", "openpyxl (>=3.0.7)", "pandas-gbq (>=0.15.0)", "psycopg2 (>=2.8.6)", "pyarrow (>=7.0.0)", "pymysql (>=1.0.2)", "pyreadstat (>=1.1.2)", "pytest (>=7.0.0)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)", "python-snappy (>=0.6.0)", "pyxlsb (>=1.0.8)", "qtpy (>=2.2.0)", "s3fs (>=2021.08.0)", "scipy (>=1.7.1)", "tables (>=3.6.1)", "tabulate (>=0.8.9)", "xarray (>=0.21.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=1.4.3)", "zstandard (>=0.15.2)"] -aws = ["s3fs (>=2021.08.0)"] -clipboard = ["PyQt5 (>=5.15.1)", "qtpy (>=2.2.0)"] -compression = ["brotlipy (>=0.7.0)", "python-snappy (>=0.6.0)", "zstandard (>=0.15.2)"] -computation = ["scipy (>=1.7.1)", "xarray (>=0.21.0)"] -excel = ["odfpy (>=1.4.1)", "openpyxl (>=3.0.7)", "pyxlsb (>=1.0.8)", "xlrd (>=2.0.1)", "xlsxwriter (>=1.4.3)"] +all = ["PyQt5 (>=5.15.6)", "SQLAlchemy (>=1.4.36)", "beautifulsoup4 (>=4.11.1)", "bottleneck (>=1.3.4)", "dataframe-api-compat (>=0.1.7)", "fastparquet (>=0.8.1)", "fsspec (>=2022.05.0)", "gcsfs (>=2022.05.0)", "html5lib (>=1.1)", "hypothesis (>=6.46.1)", "jinja2 (>=3.1.2)", "lxml (>=4.8.0)", "matplotlib (>=3.6.1)", "numba (>=0.55.2)", "numexpr (>=2.8.0)", "odfpy (>=1.4.1)", "openpyxl (>=3.0.10)", "pandas-gbq (>=0.17.5)", "psycopg2 (>=2.9.3)", "pyarrow (>=7.0.0)", "pymysql (>=1.0.2)", "pyreadstat (>=1.1.5)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)", "pyxlsb (>=1.0.9)", "qtpy (>=2.2.0)", "s3fs (>=2022.05.0)", "scipy (>=1.8.1)", "tables (>=3.7.0)", "tabulate (>=0.8.10)", "xarray (>=2022.03.0)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.3)", "zstandard (>=0.17.0)"] +aws = ["s3fs (>=2022.05.0)"] +clipboard = ["PyQt5 (>=5.15.6)", "qtpy (>=2.2.0)"] +compression = ["zstandard (>=0.17.0)"] +computation = ["scipy (>=1.8.1)", "xarray (>=2022.03.0)"] +consortium-standard = ["dataframe-api-compat (>=0.1.7)"] +excel = ["odfpy (>=1.4.1)", "openpyxl (>=3.0.10)", "pyxlsb (>=1.0.9)", "xlrd (>=2.0.1)", "xlsxwriter (>=3.0.3)"] feather = ["pyarrow (>=7.0.0)"] -fss = ["fsspec (>=2021.07.0)"] -gcp = ["gcsfs (>=2021.07.0)", "pandas-gbq (>=0.15.0)"] -hdf5 = ["tables (>=3.6.1)"] -html = ["beautifulsoup4 (>=4.9.3)", "html5lib (>=1.1)", "lxml (>=4.6.3)"] -mysql = ["SQLAlchemy (>=1.4.16)", "pymysql (>=1.0.2)"] -output-formatting = ["jinja2 (>=3.0.0)", "tabulate (>=0.8.9)"] +fss = ["fsspec (>=2022.05.0)"] +gcp = ["gcsfs (>=2022.05.0)", "pandas-gbq (>=0.17.5)"] +hdf5 = ["tables (>=3.7.0)"] +html = ["beautifulsoup4 (>=4.11.1)", "html5lib (>=1.1)", "lxml (>=4.8.0)"] +mysql = ["SQLAlchemy (>=1.4.36)", "pymysql (>=1.0.2)"] +output-formatting = ["jinja2 (>=3.1.2)", "tabulate (>=0.8.10)"] parquet = ["pyarrow (>=7.0.0)"] -performance = ["bottleneck (>=1.3.2)", "numba (>=0.53.1)", "numexpr (>=2.7.1)"] +performance = ["bottleneck (>=1.3.4)", "numba (>=0.55.2)", "numexpr (>=2.8.0)"] plot = ["matplotlib (>=3.6.1)"] -postgresql = ["SQLAlchemy (>=1.4.16)", "psycopg2 (>=2.8.6)"] -spss = ["pyreadstat (>=1.1.2)"] -sql-other = ["SQLAlchemy (>=1.4.16)"] -test = ["hypothesis (>=6.34.2)", "pytest (>=7.0.0)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)"] -xml = ["lxml (>=4.6.3)"] +postgresql = ["SQLAlchemy (>=1.4.36)", "psycopg2 (>=2.9.3)"] +spss = ["pyreadstat (>=1.1.5)"] +sql-other = ["SQLAlchemy (>=1.4.36)"] +test = ["hypothesis (>=6.46.1)", "pytest (>=7.3.2)", "pytest-asyncio (>=0.17.0)", "pytest-xdist (>=2.2.0)"] +xml = ["lxml (>=4.8.0)"] [[package]] name = "parso" @@ -945,7 +971,7 @@ testing = ["docopt", "pytest (<6.0.0)"] [[package]] name = "pathspec" -version = "0.10.2" +version = "0.11.2" description = "Utility library for gitignore style pattern matching of file paths." category = "dev" optional = false @@ -972,35 +998,35 @@ python-versions = "*" [[package]] name = "pillow" -version = "9.3.0" +version = "10.0.0" description = "Python Imaging Library (Fork)" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] -docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-issues (>=3.0.1)", "sphinx-removed-in", "sphinxext-opengraph"] +docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"] tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"] [[package]] name = "platformdirs" -version = "2.6.0" +version = "3.10.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." category = "dev" optional = false python-versions = ">=3.7" [package.extras] -docs = ["furo (>=2022.9.29)", "proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.4)"] -test = ["appdirs (==1.4.4)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)"] +docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"] +test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"] [[package]] name = "pluggy" -version = "1.0.0" +version = "1.3.0" description = "plugin and hook calling mechanisms for python" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" [package.extras] dev = ["pre-commit", "tox"] @@ -1008,7 +1034,7 @@ testing = ["pytest", "pytest-benchmark"] [[package]] name = "pre-commit" -version = "2.20.0" +version = "2.21.0" description = "A framework for managing and maintaining multi-language pre-commit hooks." category = "dev" optional = false @@ -1019,23 +1045,22 @@ cfgv = ">=2.0.0" identify = ">=1.0.0" nodeenv = ">=0.11.1" pyyaml = ">=5.1" -toml = "*" -virtualenv = ">=20.0.8" +virtualenv = ">=20.10.0" [[package]] name = "prompt-toolkit" -version = "3.0.36" +version = "3.0.39" description = "Library for building powerful interactive command lines in Python" category = "dev" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.7.0" [package.dependencies] wcwidth = "*" [[package]] name = "psutil" -version = "5.9.4" +version = "5.9.5" description = "Cross-platform lib for process and system monitoring in Python." category = "dev" optional = false @@ -1063,14 +1088,6 @@ python-versions = "*" [package.extras] tests = ["pytest"] -[[package]] -name = "py" -version = "1.11.0" -description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" - [[package]] name = "pybtex" version = "0.24.0" @@ -1089,14 +1106,14 @@ test = ["pytest"] [[package]] name = "pybtex-docutils" -version = "1.0.2" +version = "1.0.3" description = "A docutils backend for pybtex." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] -docutils = ">=0.8" +docutils = ">=0.14" pybtex = ">=0.16" [[package]] @@ -1117,17 +1134,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pydocstyle" -version = "6.1.1" +version = "6.3.0" description = "Python docstring style checker" category = "dev" optional = false python-versions = ">=3.6" [package.dependencies] -snowballstemmer = "*" +snowballstemmer = ">=2.2.0" [package.extras] -toml = ["toml"] +toml = ["tomli (>=1.2.3)"] [[package]] name = "pyflakes" @@ -1139,11 +1156,11 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pygments" -version = "2.13.0" +version = "2.16.1" description = "Pygments is a syntax highlighting package written in Python." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] plugins = ["importlib-metadata"] @@ -1159,24 +1176,15 @@ python-versions = ">=3.6.8" [package.extras] diagrams = ["jinja2", "railroad-diagrams"] -[[package]] -name = "pyrsistent" -version = "0.19.2" -description = "Persistent/Functional/Immutable data structures" -category = "dev" -optional = false -python-versions = ">=3.7" - [[package]] name = "pytest" -version = "7.2.0" +version = "7.4.1" description = "pytest: simple powerful testing with Python" category = "dev" optional = false python-versions = ">=3.7" [package.dependencies] -attrs = ">=19.2.0" colorama = {version = "*", markers = "sys_platform == \"win32\""} exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""} iniconfig = "*" @@ -1185,7 +1193,7 @@ pluggy = ">=0.12,<2.0" tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} [package.extras] -testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"] +testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"] [[package]] name = "pytest-cov" @@ -1216,7 +1224,7 @@ pytest = ">=7.0" [[package]] name = "pytest-mock" -version = "3.10.0" +version = "3.11.1" description = "Thin-wrapper around the mock package for easier use with pytest" category = "dev" optional = false @@ -1258,7 +1266,7 @@ six = ">=1.5" [[package]] name = "pytz" -version = "2022.6" +version = "2023.3.post1" description = "World timezone definitions, modern and historical" category = "dev" optional = false @@ -1266,7 +1274,7 @@ python-versions = "*" [[package]] name = "pywin32" -version = "305" +version = "306" description = "Python for Window Extensions" category = "dev" optional = false @@ -1274,7 +1282,7 @@ python-versions = "*" [[package]] name = "pyyaml" -version = "6.0" +version = "6.0.1" description = "YAML parser and emitter for Python" category = "dev" optional = false @@ -1282,7 +1290,7 @@ python-versions = ">=3.6" [[package]] name = "pyzmq" -version = "24.0.1" +version = "25.1.1" description = "Python bindings for 0MQ" category = "dev" optional = false @@ -1290,58 +1298,77 @@ python-versions = ">=3.6" [package.dependencies] cffi = {version = "*", markers = "implementation_name == \"pypy\""} -py = {version = "*", markers = "implementation_name == \"pypy\""} + +[[package]] +name = "referencing" +version = "0.30.2" +description = "JSON Referencing + Python" +category = "dev" +optional = false +python-versions = ">=3.8" + +[package.dependencies] +attrs = ">=22.2.0" +rpds-py = ">=0.7.0" [[package]] name = "requests" -version = "2.28.1" +version = "2.31.0" description = "Python HTTP for Humans." category = "dev" optional = false -python-versions = ">=3.7, <4" +python-versions = ">=3.7" [package.dependencies] certifi = ">=2017.4.17" -charset-normalizer = ">=2,<3" +charset-normalizer = ">=2,<4" idna = ">=2.5,<4" -urllib3 = ">=1.21.1,<1.27" +urllib3 = ">=1.21.1,<3" [package.extras] socks = ["PySocks (>=1.5.6,!=1.5.7)"] use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] +[[package]] +name = "rpds-py" +version = "0.10.2" +description = "Python bindings to Rust's persistent data structures (rpds)" +category = "dev" +optional = false +python-versions = ">=3.8" + [[package]] name = "scipy" -version = "1.9.3" +version = "1.11.2" description = "Fundamental algorithms for scientific computing in Python" category = "main" optional = false -python-versions = ">=3.8" +python-versions = "<3.13,>=3.9" [package.dependencies] -numpy = ">=1.18.5,<1.26.0" +numpy = ">=1.21.6,<1.28.0" [package.extras] -dev = ["flake8", "mypy", "pycodestyle", "typing_extensions"] -doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-panels (>=0.5.2)", "sphinx-tabs"] -test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] +dev = ["click", "cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyle", "pydevtool", "rich-click", "ruff", "types-psutil", "typing_extensions"] +doc = ["jupytext", "matplotlib (>2)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"] +test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"] [[package]] name = "setuptools" -version = "65.6.3" +version = "68.1.2" description = "Easily download, build, install, upgrade, and uninstall Python packages" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"] -testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5,<=7.1.2)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"] +testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] [[package]] name = "setuptools-scm" -version = "7.0.5" +version = "7.1.0" description = "the blessed package to manage your versions by scm tags" category = "dev" optional = false @@ -1350,7 +1377,7 @@ python-versions = ">=3.7" [package.dependencies] packaging = ">=20.0" setuptools = "*" -tomli = ">=1.0.0" +tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""} typing-extensions = "*" [package.extras] @@ -1425,15 +1452,16 @@ testing = ["coverage", "pytest (>=7.1,<8.0)", "pytest-cov", "pytest-regressions" [[package]] name = "sphinx-rtd-theme" -version = "1.1.1" +version = "1.3.0" description = "Read the Docs theme for Sphinx" category = "dev" optional = false -python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" [package.dependencies] -docutils = "<0.18" -sphinx = ">=1.6,<6" +docutils = "<0.19" +sphinx = ">=1.6,<8" +sphinxcontrib-jquery = ">=4,<5" [package.extras] dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"] @@ -1457,11 +1485,14 @@ sphinx = ["matplotlib", "myst-nb", "numpy", "sphinx-book-theme", "sphinx-design" [[package]] name = "sphinxcontrib-applehelp" -version = "1.0.2" -description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books" +version = "1.0.7" +description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.9" + +[package.dependencies] +Sphinx = ">=5" [package.extras] lint = ["docutils-stubs", "flake8", "mypy"] @@ -1469,26 +1500,29 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-bibtex" -version = "2.5.0" +version = "2.6.1" description = "Sphinx extension for BibTeX style citations." category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] -docutils = ">=0.8" +docutils = ">=0.8,<0.18.0 || >=0.20.0" importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""} pybtex = ">=0.24" pybtex-docutils = ">=1.0.0" -Sphinx = ">=2.1" +Sphinx = ">=3.5" [[package]] name = "sphinxcontrib-devhelp" -version = "1.0.2" -description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document." +version = "1.0.5" +description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.9" + +[package.dependencies] +Sphinx = ">=5" [package.extras] lint = ["docutils-stubs", "flake8", "mypy"] @@ -1496,16 +1530,30 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-htmlhelp" -version = "2.0.0" +version = "2.0.4" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.9" + +[package.dependencies] +Sphinx = ">=5" [package.extras] lint = ["docutils-stubs", "flake8", "mypy"] test = ["html5lib", "pytest"] +[[package]] +name = "sphinxcontrib-jquery" +version = "4.1" +description = "Extension to include jQuery on newer Sphinx releases" +category = "dev" +optional = false +python-versions = ">=2.7" + +[package.dependencies] +Sphinx = ">=1.8" + [[package]] name = "sphinxcontrib-jsmath" version = "1.0.1" @@ -1519,11 +1567,14 @@ test = ["flake8", "mypy", "pytest"] [[package]] name = "sphinxcontrib-qthelp" -version = "1.0.3" -description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document." +version = "1.0.6" +description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.9" + +[package.dependencies] +Sphinx = ">=5" [package.extras] lint = ["docutils-stubs", "flake8", "mypy"] @@ -1531,11 +1582,14 @@ test = ["pytest"] [[package]] name = "sphinxcontrib-serializinghtml" -version = "1.1.5" -description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." +version = "1.1.9" +description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)" category = "dev" optional = false -python-versions = ">=3.5" +python-versions = ">=3.9" + +[package.dependencies] +Sphinx = ">=5" [package.extras] lint = ["docutils-stubs", "flake8", "mypy"] @@ -1543,7 +1597,7 @@ test = ["pytest"] [[package]] name = "sqlalchemy" -version = "1.4.44" +version = "1.4.49" description = "Database Abstraction Library" category = "dev" optional = false @@ -1600,14 +1654,6 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.extras] widechars = ["wcwidth"] -[[package]] -name = "toml" -version = "0.10.2" -description = "Python Library for Tom's Obvious, Minimal Language" -category = "dev" -optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" - [[package]] name = "tomli" version = "2.0.1" @@ -1618,15 +1664,15 @@ python-versions = ">=3.7" [[package]] name = "tornado" -version = "6.2" +version = "6.3.3" description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." category = "dev" optional = false -python-versions = ">= 3.7" +python-versions = ">= 3.8" [[package]] name = "traitlets" -version = "5.7.0" +version = "5.9.0" description = "Traitlets Python configuration system" category = "dev" optional = false @@ -1634,13 +1680,11 @@ python-versions = ">=3.7" [package.extras] docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"] -lint = ["black (>=22.6.0)", "mdformat (>0.7)", "ruff (>=0.0.156)"] -test = ["pre-commit", "pytest"] -typing = ["mypy (>=0.990)"] +test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] [[package]] name = "types-tabulate" -version = "0.9.0.0" +version = "0.9.0.3" description = "Typing stubs for tabulate" category = "dev" optional = false @@ -1648,7 +1692,7 @@ python-versions = "*" [[package]] name = "typing-extensions" -version = "4.4.0" +version = "4.7.1" description = "Backported and Experimental Type Hints for Python 3.7+" category = "dev" optional = false @@ -1664,37 +1708,38 @@ python-versions = ">=2" [[package]] name = "urllib3" -version = "1.26.13" +version = "2.0.4" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.7" [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"] -secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] -socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] +brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"] +socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] +zstd = ["zstandard (>=0.18.0)"] [[package]] name = "virtualenv" -version = "20.17.1" +version = "20.24.4" description = "Virtual Python Environment builder" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] -distlib = ">=0.3.6,<1" -filelock = ">=3.4.1,<4" -platformdirs = ">=2.4,<3" +distlib = ">=0.3.7,<1" +filelock = ">=3.12.2,<4" +platformdirs = ">=3.9.1,<4" [package.extras] -docs = ["proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-argparse (>=0.3.2)", "sphinx-rtd-theme (>=1)", "towncrier (>=22.8)"] -testing = ["coverage (>=6.2)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=21.3)", "pytest (>=7.0.1)", "pytest-env 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= ">=3.7" [package.extras] -test = ["pytest (>=3.0.0)"] +test = ["pytest (>=6.0.0)", "setuptools (>=65)"] [[package]] name = "xarray" -version = "2023.4.0" +version = "2023.8.0" description = "N-D labeled arrays and datasets in Python" category = "dev" optional = false @@ -1734,45 +1779,45 @@ viz = ["matplotlib", "nc-time-axis", "seaborn"] [[package]] name = "zipp" -version = "3.11.0" +version = "3.16.2" description = "Backport of pathlib-compatible object wrapper for zip files" category = "dev" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] -testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", 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9aefa76c2725f9db8cb7398a753bb77b63bfe957 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 5 Sep 2023 20:20:21 +0100 Subject: [PATCH 34/39] Sphinx nitpick ignore _ScalarType_co, whatever _that_ is. --- docs/source/conf.py | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/conf.py b/docs/source/conf.py index a3cec0dc..f19a6be7 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -84,6 +84,7 @@ class MyReferenceStyle(AuthorYearReferenceStyle): # Cross-reference checking nitpicky = True nitpick_ignore = [ + ("py:class", "numpy._typing._array_like._ScalarType_co"), ("py:class", "numpy._typing._generic_alias.ScalarType"), ("py:class", "numpy.float32"), ("py:class", "numpy.timedelta64"), From 2ceb47d6c55b8db060bb09131d8ff414258899a5 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 5 Sep 2023 20:20:57 +0100 Subject: [PATCH 35/39] Extend CI to include Python 3.11 (and use 3.11 not 3.9 for QA and docs) --- .github/workflows/pyrealm_ci.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pyrealm_ci.yaml b/.github/workflows/pyrealm_ci.yaml index b60954a3..e7a3145e 100644 --- a/.github/workflows/pyrealm_ci.yaml +++ b/.github/workflows/pyrealm_ci.yaml @@ -9,7 +9,7 @@ jobs: - uses: actions/checkout@v3 - uses: actions/setup-python@v4 with: - python-version: "3.9" + python-version: "3.11" - uses: pre-commit/action@v3.0.0 test: @@ -19,7 +19,7 @@ jobs: fail-fast: false matrix: os: [ ubuntu-latest, macos-latest, windows-latest ] - python-version: [ "3.9" , "3.10"] + python-version: [ "3.9" , "3.10", "3.11"] steps: - uses: actions/checkout@v3 @@ -50,7 +50,7 @@ jobs: - uses: actions/checkout@v3 - uses: actions/setup-python@v4 with: - python-version: "3.9" + python-version: "3.11" - name: Install Poetry uses: abatilo/actions-poetry@v2.1.6 From 9e23b2980ac265ba7d93cef08b0fd5b847ab9397 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 5 Sep 2023 21:07:37 +0100 Subject: [PATCH 36/39] Update docs build job to archive built docs for 1 day for error checking --- .github/workflows/pyrealm_ci.yaml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pyrealm_ci.yaml b/.github/workflows/pyrealm_ci.yaml index e7a3145e..234f17db 100644 --- a/.github/workflows/pyrealm_ci.yaml +++ b/.github/workflows/pyrealm_ci.yaml @@ -66,4 +66,11 @@ jobs: - name: Build docs using sphinx run: | cd docs - poetry run sphinx-build -W --keep-going source build \ No newline at end of file + poetry run sphinx-build -W --keep-going source build + + - name: Archive built docs for error checking + uses: actions/upload-artifact@v3 + with: + name: built-docs + path: docs/build + retention-days: 2 From 5f68c01afec4a0f4cdccbd55eded27a78c6b3189 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 5 Sep 2023 21:13:22 +0100 Subject: [PATCH 37/39] Save doc build artefacts on build _failure_ --- .github/workflows/pyrealm_ci.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pyrealm_ci.yaml b/.github/workflows/pyrealm_ci.yaml index 234f17db..372d6301 100644 --- a/.github/workflows/pyrealm_ci.yaml +++ b/.github/workflows/pyrealm_ci.yaml @@ -68,7 +68,8 @@ jobs: cd docs poetry run sphinx-build -W --keep-going source build - - name: Archive built docs for error checking + - name: Archive built docs for error checking on failure + if: failure() uses: actions/upload-artifact@v3 with: name: built-docs From 83bbfe0be2a005eebaa790501b747d13bcf55fb3 Mon Sep 17 00:00:00 2001 From: David Orme Date: Tue, 5 Sep 2023 21:25:04 +0100 Subject: [PATCH 38/39] Fix issue with printing results in lue_limitation.md --- .../users/pmodel/pmodel_details/lue_limitation.md | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/docs/source/users/pmodel/pmodel_details/lue_limitation.md b/docs/source/users/pmodel/pmodel_details/lue_limitation.md index ab9f4e3e..594f0663 100644 --- a/docs/source/users/pmodel/pmodel_details/lue_limitation.md +++ b/docs/source/users/pmodel/pmodel_details/lue_limitation.md @@ -104,12 +104,20 @@ dependency of $\phi_0$. ```{code-cell} env = PModelEnvironment(tc=30, patm=101325, vpd=820, co2=400) model_fixkphio = PModel(env, kphio=0.08, do_ftemp_kphio=False) -np.array([model_fixkphio.init_kphio, model_fixkphio.kphio]) +model_fixkphio.init_kphio +``` + +```{code-cell} +model_fixkphio.kphio ``` ```{code-cell} model_tempkphio = PModel(env, kphio=0.08, do_ftemp_kphio=True) -np.array([model_tempkphio.init_kphio, model_tempkphio.kphio]) +model_fixkphio.init_kphio +``` + +```{code-cell} +model_fixkphio.kphio ``` The scaling of temperature dependence varies for C3 and C4 plants and the function From d6792ee1436a8daa14e7db1e26038d9457508dfa Mon Sep 17 00:00:00 2001 From: davidorme Date: Mon, 11 Sep 2023 00:04:16 +0000 Subject: [PATCH 39/39] chore: update pre-commit hooks --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8691e9f8..08269ca7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,7 +10,7 @@ repos: - id: isort additional_dependencies: [toml] - repo: https://github.com/psf/black - rev: "23.7.0" + rev: "23.9.0" hooks: - id: black - repo: https://github.com/PyCQA/flake8