diff --git a/.copier-answers.yml b/.copier-answers.yml new file mode 100644 index 0000000..1a2bce3 --- /dev/null +++ b/.copier-answers.yml @@ -0,0 +1,15 @@ +# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY +_commit: v0.4.1 +_src_path: gl:znicholls/copier-core-python-repository +email: zebedee.nicholls@climate-energy-college.org +include_cli: true +name: Zebedee Nicholls +notebook_based_docs: true +pandas_doctests: false +plot_dependencies: false +project_description_short: Command-line tool for uploading to zenodo. +project_name_human: OpenSCM Zenodo +project_name_pip: openscm-zenodo +project_name_python: openscm_zenodo +project_url: https://github.com/openscm/OpenSCM-zenodo +track_lock_file: true diff --git a/.github/ISSUE_TEMPLATE/bug.md b/.github/ISSUE_TEMPLATE/bug.md index d43f709..ebc3616 100644 --- a/.github/ISSUE_TEMPLATE/bug.md +++ b/.github/ISSUE_TEMPLATE/bug.md @@ -35,7 +35,6 @@ def test_bug_12(): - OS: [e.g. Windows, Linux, macOS] - Python version [e.g. Python 3.11] - - Please also upload your `poetry.lock` file (first run `poetry lock` to make sure the lock file is up-to-date) ## Additional context diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 89da71c..81122b2 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -16,7 +16,7 @@ jobs: - uses: ./.github/actions/setup with: python-version: "3.11" - pdm-dependency-install-flags: "-G dev" + pdm-dependency-install-flags: "-G :all" - name: mypy run: | MYPYPATH=stubs pdm run mypy src @@ -30,11 +30,17 @@ jobs: - uses: ./.github/actions/setup with: python-version: "3.11" - pdm-dependency-install-flags: "-G docs -G dev" + pdm-dependency-install-flags: "-G docs -G :all" - name: docs run: | pdm run typer openscm_zenodo.cli utils docs --output docs/cli/index.md --name openscm-zenodo pdm run mkdocs build --strict + - uses: ./.github/actions/setup + with: + python-version: "3.11" + pdm-dependency-install-flags: "-G docs -G :all -G dev" + - name: docs-with-changelog + run: | # Check CHANGELOG will build too pdm run towncrier build --yes pdm run mkdocs build --strict @@ -61,11 +67,16 @@ jobs: - uses: ./.github/actions/setup with: python-version: ${{ matrix.python-version }} - pdm-dependency-install-flags: "-G tests" - # TODO: sort out zenodo token + # When running the tests, install with all optional dependencies + # to get maximum test coverage. + # If we find that we're getting failures + # when people try to run without installing optional dependencies, + # we should add a CI step that runs the tests without optional dependencies too. + # We don't have that right now, because we're not sure this pain point exists. + pdm-dependency-install-flags: "-G :all -G tests" - name: Run tests run: | - pdm run pytest -r a -v src tests --doctest-modules + pdm run pytest -r a -v src tests - name: Run tests with zenodo token # Only run these on one machine to avoid CI fighting each other by modifying the same Zenodo record if: ${{ (matrix.python-version == '3.11') && (matrix.os == 'ubuntu-latest') }} @@ -90,7 +101,7 @@ jobs: - uses: ./.github/actions/setup with: python-version: ${{ matrix.python-version }} - pdm-dependency-install-flags: "--prod" + pdm-dependency-install-flags: "--prod --without :all" - name: Check importable without extras run: pdm run python scripts/test-install.py diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index 996a93d..3133d00 100644 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -11,6 +11,10 @@ defaults: jobs: deploy-pypi: name: Deploy to PyPI + # Having an environment for deployment is strongly recommend by PyPI + # https://docs.pypi.org/trusted-publishers/adding-a-publisher/#github-actions + # You can comment this line out if you don't want it. + environment: deploy runs-on: ubuntu-latest permissions: # this permission is mandatory for trusted publishing with PyPI diff --git a/.gitignore b/.gitignore index 170f599..eb2aeeb 100644 --- a/.gitignore +++ b/.gitignore @@ -1,10 +1,28 @@ +# Notebooks +*.ipynb + +# Auto-generated docs and helper files +docs/api/* +!docs/api/.gitkeep +docs/cli/* +!docs/cli/.gitkeep + # pdm stuff .pdm-python -# CI stuff -pdm-install-flags.txt +# Databases +*.db + +# Jupyter cache +.jupyter_cache -# licence check +# IDE stuff +.idea/ + +# Ruff cache +.ruff_cache + +# Licence check licence-check.txt # Byte-compiled / optimized / DLL files @@ -136,3 +154,6 @@ dmypy.json # Pyre type checker .pyre/ + +# Mac stuff +*.DS_Store diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index adeac50..fa3c69a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,14 +3,13 @@ ci: autofix_prs: false autoupdate_schedule: quarterly autoupdate_branch: pre-commit-autoupdate - # Skip steps that won't run on pre-commit CI for various reasons, - # mostly because they rely on local things. - skip: [ ] + # Currently network access isn't supported in the pre-commit CI product. + skip: [pdm-lock-check, pdm-export, pdm-sync] # See https://pre-commit.com/hooks.html for more hooks repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: 'v4.5.0' + rev: "v4.5.0" hooks: - id: check-added-large-files - id: check-ast @@ -34,7 +33,7 @@ repos: language: fail files: "\\.rej$" - repo: https://github.com/charliermarsh/ruff-pre-commit - rev: 'v0.1.8' + rev: "v0.1.8" hooks: - id: ruff args: [ --fix, --exit-non-zero-on-fix ] @@ -43,10 +42,15 @@ repos: rev: 2.17.0 hooks: # Check that the lock file is up to date. + # We need the pdm lock file too + # so that we can build locked version of the package. - id: pdm-lock-check - args: [ --dev, --group, ":all" ] - # Put a requirements.txt file in the repo too + args: ["--dev", "-G", ":all", "--strategy", "inherit_metadata" ] + # Put requirements.txt files in the repo too - id: pdm-export - args: ['--prod', '-o', 'requirements.txt', '--without-hashes'] + name: export-requirements + args: ["-o", "requirements-locked.txt", "--without-hashes", "--prod"] + - id: pdm-export + name: export-requirements-docs + args: ["-o", "requirements-docs-locked.txt", "--without-hashes", "-G", ":all", "-G", "docs"] - id: pdm-sync - args: [ -G, ":all" ] diff --git a/.readthedocs.yml b/.readthedocs.yaml similarity index 62% rename from .readthedocs.yml rename to .readthedocs.yaml index 0924fa6..11a4ba9 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yaml @@ -2,8 +2,6 @@ # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details -# Thank you also https://browniebroke.com/blog/specify-docs-dependency-groups-with-poetry-and-read-the-docs/ - # Required version: 2 @@ -13,13 +11,10 @@ build: tools: python: "3.11" jobs: - post_create_environment: - - pip install pdm post_install: - # RtD seems to be not happy with poetry installs, + # RtD seems to be not happy with pdm installs, # hence use pip directly instead. - - pdm export -f requirements --output requirements.txt --with docs - - python -m pip install -r requirements.txt + - python -m pip install -r requirements-docs-locked.txt - python -m pip list pre_build: - pip install --no-deps . diff --git a/Makefile b/Makefile index e5b71f7..f3b115b 100644 --- a/Makefile +++ b/Makefile @@ -32,9 +32,9 @@ checks: ## run all the linting checks of the codebase ruff-fixes: ## fix the code using ruff # format before and after checking so that the formatted stuff is checked and # the fixed stuff is formatted - pdm run ruff format src tests scripts - pdm run ruff check src tests scripts --fix - pdm run ruff format src tests scripts + pdm run ruff format src tests scripts docs + pdm run ruff check src tests scripts docs --fix + pdm run ruff format src tests scripts docs .PHONY: test @@ -42,14 +42,20 @@ test: ## run the tests pdm run pytest src tests -r a -v --doctest-modules --cov=src # Note on code coverage and testing: -# You must specify cov=src as otherwise funny things happen when doctests are -# involved. -# If you want to debug what is going on with coverage, we have found -# that adding COVERAGE_DEBUG=trace to the front of the above command -# can be very helpful as it shows you if coverage is tracking the coverage +# You must specify cov=src. +# Otherwise, funny things happen when doctests are involved. +# If you want to debug what is going on with coverage, +# we have found that adding COVERAGE_DEBUG=trace +# to the front of the below command +# can be very helpful as it shows you +# if coverage is tracking the coverage # of all of the expected files or not. -# We are sure that the coverage maintainers would appreciate a PR that improves -# the coverage handling when there are doctests and a `src` layout like ours. +# We are sure that the coverage maintainers would appreciate a PR +# that improves the coverage handling when there are doctests +# and a `src` layout like ours. + +docs/cli/index.md: src/openscm_zenodo/cli/__init__.py ## auto-generate the typer app docs + pdm run typer openscm_zenodo.cli utils docs --output docs/cli/index.md --name openscm-zenodo .PHONY: docs docs: docs/cli/index.md ## build the docs @@ -63,22 +69,20 @@ docs-strict: docs/cli/index.md ## build the docs strictly (e.g. raise an error docs-serve: docs/cli/index.md ## serve the docs locally pdm run mkdocs serve -docs/cli/index.md: src/openscm_zenodo/cli/__init__.py ## auto-generate the typer app docs - pdm run typer openscm_zenodo.cli utils docs --output docs/cli/index.md --name openscm-zenodo - .PHONY: changelog-draft changelog-draft: ## compile a draft of the next changelog - pdm run towncrier build --draft + pdm run towncrier build --draft --version draft .PHONY: licence-check licence-check: ## Check that licences of the dependencies are suitable # Will likely fail on Windows, but Makefiles are in general not Windows # compatible so we're not too worried - pdm export -o $(TEMP_FILE) --without=tests --without=docs --without=dev + pdm export --without=tests --without=docs --without=dev > $(TEMP_FILE) pdm run liccheck -r $(TEMP_FILE) -R licence-check.txt - rm $(TEMP_FILE) + rm -f $(TEMP_FILE) .PHONY: virtual-environment virtual-environment: ## update virtual environment, create a new one if it doesn't already exist - pdm install -G :all + pdm lock --dev --group :all --strategy inherit_metadata + pdm install --dev --group :all pdm run pre-commit install diff --git a/README.md b/README.md index a36a70a..832d8f9 100644 --- a/README.md +++ b/README.md @@ -1,85 +1,93 @@ -# OpenSCM-Zenodo +# OpenSCM Zenodo -Validation of input4MIPs data (checking file formats, metadata etc.). +Command-line tool for uploading to zenodo. **Key info :** [![Docs](https://readthedocs.org/projects/openscm-zenodo/badge/?version=latest)](https://openscm-zenodo.readthedocs.io) -[![Main branch: supported Python versions](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fopenscm%2Fopenscm-zenodo%2Fmain%2Fpyproject.toml)](https://github.com/openscm/openscm-zenodo/blob/main/pyproject.toml) -[![Licence](https://img.shields.io/pypi/l/openscm-zenodo?label=licence)](https://github.com/openscm/openscm-zenodo/blob/main/LICENCE) +[![Main branch: supported Python versions](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fopenscm%2FOpenSCM-zenodo%2Fmain%2Fpyproject.toml)](https://github.com/openscm/OpenSCM-zenodo/blob/main/pyproject.toml) +[![Licence](https://img.shields.io/pypi/l/openscm-zenodo?label=licence)](https://github.com/openscm/OpenSCM-zenodo/blob/main/LICENCE) **PyPI :** [![PyPI](https://img.shields.io/pypi/v/openscm-zenodo.svg)](https://pypi.org/project/openscm-zenodo/) -[![PyPI install](https://github.com/openscm/openscm-zenodo/actions/workflows/install-pypi.yaml/badge.svg?branch=main)](https://github.com/openscm/openscm-zenodo/actions/workflows/install-pypi.yaml) +[![PyPI install](https://github.com/openscm/OpenSCM-zenodo/actions/workflows/install-pypi.yaml/badge.svg?branch=main)](https://github.com/openscm/OpenSCM-zenodo/actions/workflows/install-pypi.yaml) - **Tests :** -[![CI](https://github.com/openscm/openscm-zenodo/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/openscm/openscm-zenodo/actions/workflows/ci.yaml) -[![Coverage](https://codecov.io/gh/openscm/openscm-zenodo/branch/main/graph/badge.svg)](https://codecov.io/gh/openscm/openscm-zenodo) +[![CI](https://github.com/openscm/OpenSCM-zenodo/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/openscm/OpenSCM-zenodo/actions/workflows/ci.yaml) +[![Coverage](https://codecov.io/gh/openscm/OpenSCM-zenodo/branch/main/graph/badge.svg)](https://codecov.io/gh/openscm/OpenSCM-zenodo) **Other info :** -[![Last Commit](https://img.shields.io/github/last-commit/openscm/openscm-zenodo.svg)](https://github.com/openscm/openscm-zenodo/commits/main) -[![Contributors](https://img.shields.io/github/contributors/openscm/openscm-zenodo.svg)](https://github.com/openscm/openscm-zenodo/graphs/contributors) +[![Last Commit](https://img.shields.io/github/last-commit/openscm/OpenSCM-zenodo.svg)](https://github.com/openscm/OpenSCM-zenodo/commits/main) +[![Contributors](https://img.shields.io/github/contributors/openscm/OpenSCM-zenodo.svg)](https://github.com/openscm/OpenSCM-zenodo/graphs/contributors) ## Status + + - development: the project is actively being worked on +Full documentation can be found at: +[openscm-zenodo.readthedocs.io](https://openscm-zenodo.readthedocs.io/en/latest/). +We recommend reading the docs there because the internal documentation links +don't render correctly on GitHub's viewer. + ## Installation ### As an application -If you want to use openscm-zenodo as an application, -for example you just want to use its command-line interface, +If you want to use OpenSCM Zenodo as an application, then we recommend using the 'locked' version of the package. This version pins the version of all dependencies too, which reduces the chance of installation issues because of breaking updates to dependencies. -The locked version of openscm-zenodo can be installed with +The locked version of OpenSCM Zenodo can be installed with - - === "pip" ```sh pip install openscm-zenodo[locked] ``` - [pip](https://pip.pypa.io/en/stable/) - is a standard way to install Python packages. - ### As a library -If you want to use openscm-zenodo as a library, +If you want to use OpenSCM Zenodo as a library, for example you want to use it as a dependency in another package/application that you're building, then we recommend installing the package with the commands below. @@ -87,68 +95,32 @@ This method provides the loosest pins possible of all dependencies. This gives you, the package/application developer, as much freedom as possible to set the versions of different packages. However, the tradeoff with this freedom is that you may install -incompatible versions of openscm-zenodo's dependencies +incompatible versions of OpenSCM Zenodo's dependencies (we cannot test all combinations of dependencies, particularly ones which haven't been released yet!). Hence, you may run into installation issues. -If you believe these are because of a problem in openscm-zenodo, -please [raise an issue](https://github.com/openscm/openscm-zenodo/issues/new/choose). +If you believe these are because of a problem in OpenSCM Zenodo, +please [raise an issue](https://github.com/openscm/OpenSCM-zenodo/issues). -The (non-locked) version of openscm-zenodo can be installed with +The (non-locked) version of OpenSCM Zenodo can be installed with - - === "pip" ```sh pip install openscm-zenodo ``` - [pip](https://pip.pypa.io/en/stable/) - is a standard way to install Python packages. - We make no guarantees that this will actually work - because pip's handling of the compiled dependencies - is not guaranteed. - -Additional dependencies can be installed using - - - -=== "pip" - ```sh - # To add notebook dependencies - pip install openscm-zenodo[notebooks] - ``` - ### For developers For development, we rely on [pdm](https://pdm-project.org/en/latest/) @@ -163,10 +135,17 @@ You can read the instructions out and run the commands by hand if you wish, but we generally discourage this because it can be error prone. In order to create your environment, run `make virtual-environment`. -If there are any issues, the messages from the `Makefile` should guide you -through. If not, please raise an issue in the -[issue tracker](https://github.com/openscm/openscm-zenodo/issues). +If there are any issues, the messages from the `Makefile` should guide you through. +If not, please raise an issue in the +[issue tracker](https://github.com/openscm/OpenSCM-zenodo/issues). -For the rest of our developer docs, please see [development][development-reference]. +For the rest of our developer docs, please see [development][development]. + +## Original template + +This project was generated from this template: +[copier core python repository](https://gitlab.com/znicholls/copier-core-python-repository). +[copier](https://copier.readthedocs.io/en/stable/) is used to manage and +distribute this template. diff --git a/changelog/14.trivial.md b/changelog/14.trivial.md new file mode 100644 index 0000000..26bbf84 --- /dev/null +++ b/changelog/14.trivial.md @@ -0,0 +1 @@ +Switch to using a copier template to manage the repo's structure. diff --git a/changelog/README.md b/changelog/README.md index 41ad186..10797f0 100644 --- a/changelog/README.md +++ b/changelog/README.md @@ -1,11 +1,14 @@ # CHANGELOG -This directory contains "news fragments", i.e. short files that contain a small markdown-formatted bit of text that will be -added to the CHANGELOG when it is next compiled. +This directory contains "news fragments", +i.e. short files that contain a small markdown-formatted bit of text +that will be added to the CHANGELOG when it is next compiled. -The CHANGELOG will be read by users, so this description should be aimed to Input4MIPs-validation users instead of -describing internal changes which are only relevant to developers. Merge requests in combination with our git history provides additional -developer-centric information. +The CHANGELOG will be read by users, +so this description should be aimed to OpenSCM Zenodo users +instead of describing internal changes which are only relevant to developers. +Merge requests in combination with our git history +provide additional developer-centric information. Make sure to use phrases in the past tense and use punctuation, examples: @@ -27,15 +30,18 @@ Each file should have a name of the form `..md`, where `` is the m So for example: `123.feature.md`, `456.fix.md`. -Since you need the merge request number for the filename, you must submit a MR first. From this MR, you can get the MR number and then create the news file. A single MR can also have multiple news items, for example a given MR may add a feature as well as -deprecate some existing functionality. +Since you need the merge request number for the filename, you must submit a MR first. +From this MR, you can get the MR number and then create the news file. +A single MR can also have multiple news items, +for example a given MR may add a feature as well as deprecate some existing functionality. If you are not sure what issue type to use, don't hesitate to ask in your MR. -`towncrier` preserves multiple paragraphs and formatting (code blocks, lists, and so on), but for entries other than -features it is usually better to stick to a single paragraph to keep it concise. You may also use `MyST` [style -cross-referencing](https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html) within your news items to link to other -documentation. +`towncrier` preserves multiple paragraphs and formatting +(code blocks, lists, and so on), +but for entries other than features it is usually better to stick to a single paragraph to keep it concise. +You may also use [mkdocs-autorefs cross-referencing](https://mkdocstrings.github.io/autorefs/) +within your news items to link to other documentation. -You can also run `towncrier build --draft` to see the draft changelog that will be appended to [docs/source/changelog.md]() -on the next release. +You can also run `towncrier build --draft --version draft` +to see the draft changelog that will be appended to the CHANGELOG on the next release. diff --git a/docs/NAVIGATION.md b/docs/NAVIGATION.md new file mode 100644 index 0000000..6fea3d5 --- /dev/null +++ b/docs/NAVIGATION.md @@ -0,0 +1,14 @@ + +- [Home](index.md) +- [Installation](installation.md) +- [How-to guides](how-to-guides/index.md) +- [Tutorials](tutorials/index.md) +- [Further background](further-background/index.md) +- [Development](development.md) +- [Command-line interface](cli/index.md) +- [API reference](api/openscm_zenodo/) +- [Changelog](changelog.md) diff --git a/docs/api/.gitkeep b/docs/api/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/docs/changelog.md b/docs/changelog.md index 1fa5464..a7aece1 100644 --- a/docs/changelog.md +++ b/docs/changelog.md @@ -5,21 +5,23 @@ Versions follow [Semantic Versioning](https://semver.org/) (`.. -## OpenSCM-Zenodo v0.3.0 (2024-08-25) +## OpenSCM Zenodo v0.3.0 (2024-08-25) ### 🆕 Features @@ -27,57 +29,57 @@ of rst and use slightly different categories. - Added bibtex metadata retrieval. Specifically: `openscm-zenodo retrieve-bibtex`, [`retrieve_bibtex_entry`][openscm_zenodo.zenodo.retrieve_bibtex_entry] - and [`get_bibtex_entry`][openscm_zenodo.zenodo.ZenodoInteractor.get_bibtex_entry]. ([#12](https://github.com/climate-resource/input4mips_validation/pulls/12)) + and [`get_bibtex_entry`][openscm_zenodo.zenodo.ZenodoInteractor.get_bibtex_entry]. ([#12](https://github.com/openscm/openscm-zenodo/pull/12)) ### 🎉 Improvements -- Added support for parallel uploads to `openscm-zenodo create-new-version`. ([#12](https://github.com/climate-resource/input4mips_validation/pulls/12)) +- Added support for parallel uploads to `openscm-zenodo create-new-version`. ([#12](https://github.com/openscm/openscm-zenodo/pull/12)) -## OpenSCM-Zenodo v0.2.6 (2024-08-22) +## OpenSCM Zenodo v0.2.6 (2024-08-22) ### 🔧 Trivial/Internal Changes -- [#11](https://github.com/climate-resource/input4mips_validation/pulls/11) +- [#11](https://github.com/openscm/openscm-zenodo/pull/11) -## OpenSCM-Zenodo v0.2.4 (2024-08-22) +## OpenSCM Zenodo v0.2.4 (2024-08-22) ### 🆕 Features - Added the `--reserve-doi` flag to the `openscm-zenodo update-metadata` command. - Also added [`get_reserved_doi`][openscm_zenodo.zenodo.get_reserved_doi]. ([#10](https://github.com/climate-resource/input4mips_validation/pulls/10)) + Also added [`get_reserved_doi`][openscm_zenodo.zenodo.get_reserved_doi]. ([#10](https://github.com/openscm/openscm-zenodo/pull/10)) ### 🔧 Trivial/Internal Changes -- [#10](https://github.com/climate-resource/input4mips_validation/pulls/10) +- [#10](https://github.com/openscm/openscm-zenodo/pull/10) -## OpenSCM-Zenodo v0.2.3 (2024-08-21) +## OpenSCM Zenodo v0.2.3 (2024-08-21) ### 🔧 Trivial/Internal Changes -- [#9](https://github.com/climate-resource/input4mips_validation/pulls/9) +- [#9](https://github.com/openscm/openscm-zenodo/pull/9) -## OpenSCM-Zenodo v0.2.2 (2024-08-21) +## OpenSCM Zenodo v0.2.2 (2024-08-21) ### 🔧 Trivial/Internal Changes -- [#8](https://github.com/climate-resource/input4mips_validation/pulls/8) +- [#8](https://github.com/openscm/openscm-zenodo/pull/8) -## OpenSCM-Zenodo v0.2.1 (2024-08-21) +## OpenSCM Zenodo v0.2.1 (2024-08-21) No significant changes. -## OpenSCM-Zenodo v0.2.0 (2024-08-21) +## OpenSCM Zenodo v0.2.0 (2024-08-21) No significant changes. diff --git a/docs/cli/.gitkeep b/docs/cli/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/docs/cli/index.md b/docs/cli/index.md index 009f6db..d87c0f9 100644 --- a/docs/cli/index.md +++ b/docs/cli/index.md @@ -25,11 +25,16 @@ If supplied, this overrides any value provided with `--log-level`. **Commands**: -* `create-new-version`: Create a new version of a recod +* `create-new-version`: Create a new version of a record +* `remove-files`: Remove files from a Zenodo deposition +* `retrieve-bibtex`: Retrieve bibtex entry +* `retrieve-metadata`: Retrieve metadata +* `update-metadata`: Update metadata +* `upload-files`: Upload files to a Zenodo deposition ## `openscm-zenodo create-new-version` -Create a new version of a recod +Create a new version of a record **Usage**: @@ -40,12 +45,129 @@ $ openscm-zenodo create-new-version [OPTIONS] ANY_DEPOSITION_ID [FILES_TO_UPLOAD **Arguments**: * `ANY_DEPOSITION_ID`: A deposition ID related to the record you wish to interact with. You can pick any published deposit/version. This ID is most easily extracted from the URL provided by Zenodo. It is just the digits at the end of that link. For example, if Zenodo URL is https://zenodo.org/records/10702583, then the deposit ID is 10702583. [required] -* `[FILES_TO_UPLOAD]...`: Files to upload the the Zenodo deposition +* `[FILES_TO_UPLOAD]...`: Files to upload to the Zenodo deposition **Options**: * `--token TEXT`: Zenodo token to use for this interaction. For more information about generating tokens, see the 'Creating a personal access token' header of https://developers.zenodo.org/#authentication. [env var: ZENODO_TOKEN; required] -* `--metadata-file FILE`: Path to the `.json` file containing the metadata to use for this version. The `.json` file should have a 'metadata' key, which points to a dictionary of key : value pairs.To get an example, use the `openscm-zenodo retrieve-metadata` command. For example, `openscm-zenodo retrieve-metadata 4589756`.For the complete list of supported key : value pairs, see [https://developers.zenodo.org/#representation](). +* `--metadata-file FILE`: Path to the `.json` file containing the metadata to use for this version. The `.json` file should have a single 'metadata' key, which points to a dictionary of key : value pairs.For futher information about the required form, see the docstring of [`update_metadata`][openscm_zenodo.zenodo.ZenodoInteractor.update_metadata]. To get an example, see the docstring of [`retrieve_metadata`][openscm_zenodo.zenodo.retrieve_metadata]. * `--publish`: Publish the newly created version after creating it and uploading the files * `--zenodo-domain [https://zenodo.org|https://sandbox.zenodo.org]`: The zenodo domain with which you want to interact. [default: https://zenodo.org] +* `--n-threads INTEGER`: Number of threads to use for parallel processing [default: 4] +* `--help`: Show this message and exit. + +## `openscm-zenodo remove-files` + +Remove files from a Zenodo deposition + +**Usage**: + +```console +$ openscm-zenodo remove-files [OPTIONS] DEPOSITION_ID [FILES_TO_REMOVE]... +``` + +**Arguments**: + +* `DEPOSITION_ID`: The ID of the deposition you wish to interact with. This ID is most easily extracted from the URL provided by Zenodo. It is just the digits at the end of that link. For example, if Zenodo URL is https://zenodo.org/records/10702583, then the deposition ID is 10702583. [required] +* `[FILES_TO_REMOVE]...`: Files to remove from the Zenodo deposition + +**Options**: + +* `--token TEXT`: Zenodo token to use for this interaction. For more information about generating tokens, see the 'Creating a personal access token' header of https://developers.zenodo.org/#authentication. [env var: ZENODO_TOKEN; required] +* `--all`: Remove all files +* `--zenodo-domain [https://zenodo.org|https://sandbox.zenodo.org]`: The zenodo domain with which you want to interact. [default: https://zenodo.org] +* `--help`: Show this message and exit. + +## `openscm-zenodo retrieve-bibtex` + +Retrieve bibtex entry + +**Usage**: + +```console +$ openscm-zenodo retrieve-bibtex [OPTIONS] DEPOSITION_ID +``` + +**Arguments**: + +* `DEPOSITION_ID`: The ID of the deposition you wish to interact with. This ID is most easily extracted from the URL provided by Zenodo. It is just the digits at the end of that link. For example, if Zenodo URL is https://zenodo.org/records/10702583, then the deposition ID is 10702583. [required] + +**Options**: + +* `--token TEXT`: Zenodo token to use for this interaction. For more information about generating tokens, see the 'Creating a personal access token' header of https://developers.zenodo.org/#authentication. [env var: ZENODO_TOKEN] +* `--zenodo-domain [https://zenodo.org|https://sandbox.zenodo.org]`: The zenodo domain with which you want to interact. [default: https://zenodo.org] +* `--help`: Show this message and exit. + +## `openscm-zenodo retrieve-metadata` + +Retrieve metadata + +**Usage**: + +```console +$ openscm-zenodo retrieve-metadata [OPTIONS] DEPOSITION_ID +``` + +**Arguments**: + +* `DEPOSITION_ID`: The ID of the deposition you wish to interact with. This ID is most easily extracted from the URL provided by Zenodo. It is just the digits at the end of that link. For example, if Zenodo URL is https://zenodo.org/records/10702583, then the deposition ID is 10702583. [required] + +**Options**: + +* `--token TEXT`: Zenodo token to use for this interaction. For more information about generating tokens, see the 'Creating a personal access token' header of https://developers.zenodo.org/#authentication. [env var: ZENODO_TOKEN] +* `--user-controlled-only / --no-user-controlled-only`: Only return metadata keys that the user can control. + +If this is `True`, the metadata keys controlled by Zenodo (e.g. the DOI) +are removed from the returned metadata. +This flag is important to use +if you want to use the retrieved metadata +as the starting point for the next version of a deposit. [default: no-user-controlled-only] +* `--zenodo-domain [https://zenodo.org|https://sandbox.zenodo.org]`: The zenodo domain with which you want to interact. [default: https://zenodo.org] +* `--help`: Show this message and exit. + +## `openscm-zenodo update-metadata` + +Update metadata + +If the `--reserve-doi` flag is used, +this prints the reserved DOI to stdout. + +**Usage**: + +```console +$ openscm-zenodo update-metadata [OPTIONS] DEPOSITION_ID +``` + +**Arguments**: + +* `DEPOSITION_ID`: The ID of the deposition you wish to interact with. This ID is most easily extracted from the URL provided by Zenodo. It is just the digits at the end of that link. For example, if Zenodo URL is https://zenodo.org/records/10702583, then the deposition ID is 10702583. [required] + +**Options**: + +* `--metadata-file FILE`: Path to the `.json` file containing the metadata to use for this version. The `.json` file should have a single 'metadata' key, which points to a dictionary of key : value pairs.For futher information about the required form, see the docstring of [`update_metadata`][openscm_zenodo.zenodo.ZenodoInteractor.update_metadata]. To get an example, see the docstring of [`retrieve_metadata`][openscm_zenodo.zenodo.retrieve_metadata]. [required] +* `--token TEXT`: Zenodo token to use for this interaction. For more information about generating tokens, see the 'Creating a personal access token' header of https://developers.zenodo.org/#authentication. [env var: ZENODO_TOKEN; required] +* `--zenodo-domain [https://zenodo.org|https://sandbox.zenodo.org]`: The zenodo domain with which you want to interact. [default: https://zenodo.org] +* `--reserve-doi`: Reserve a DOI while updating the metadata. This will overwrite any value in the metadata file supplied. +* `--help`: Show this message and exit. + +## `openscm-zenodo upload-files` + +Upload files to a Zenodo deposition + +**Usage**: + +```console +$ openscm-zenodo upload-files [OPTIONS] DEPOSITION_ID FILES_TO_UPLOAD... +``` + +**Arguments**: + +* `DEPOSITION_ID`: The ID of the deposition you wish to interact with. This ID is most easily extracted from the URL provided by Zenodo. It is just the digits at the end of that link. For example, if Zenodo URL is https://zenodo.org/records/10702583, then the deposition ID is 10702583. [required] +* `FILES_TO_UPLOAD...`: Files to upload to the Zenodo deposition [required] + +**Options**: + +* `--token TEXT`: Zenodo token to use for this interaction. For more information about generating tokens, see the 'Creating a personal access token' header of https://developers.zenodo.org/#authentication. [env var: ZENODO_TOKEN; required] +* `--zenodo-domain [https://zenodo.org|https://sandbox.zenodo.org]`: The zenodo domain with which you want to interact. [default: https://zenodo.org] +* `--n-threads INTEGER`: Number of threads to use for parallel processing [default: 4] * `--help`: Show this message and exit. diff --git a/docs/development.md b/docs/development.md index f258182..e0cfe85 100644 --- a/docs/development.md +++ b/docs/development.md @@ -1,7 +1,7 @@ -[](){#development-reference} # Development -Notes for developers. If you want to get involved, please do! +Notes for developers. +If you want to get involved, please do! We welcome all kinds of contributions, for example: - docs fixes/clarifications @@ -14,18 +14,17 @@ We welcome all kinds of contributions, for example: ## Workflows We don't mind whether you use a branching or forking workflow. -However, please only push to your own branches, -pushing to other people's branches is often a recipe for disaster, -is never required in our experience -so is best avoided. +However, please only push to your own branches. +Pushing to other people's branches is best avoided because +it is a recipe for disaster +and is never required in our experience. Try and keep your merge requests as small as possible (focus on one thing if you can). @@ -39,20 +38,9 @@ We do this for consistency with the broader work context of our lead developers. ## Versioning -This package follows the version format -described in [PEP440](https://peps.python.org/pep-0440/) -and [Semantic Versioning](https://semver.org/) -to describe how the version should change -depending on the updates to the code base. -Our changelog entries and compiled CHANGELOG -[TODO: docs explaining our CHANGELOG approach/reference to changelog/README.md] -allow us to identify where key changes were made. - -## Dependency management - -We manage our dependencies using [pdm](https://pdm-project.org/en/latest/). -This provides us with all the key dependency tools we need, -most notably [pdm-build-locked](https://pdm-build-locked.readthedocs.io/en/stable/). +This package follows the version format described in [PEP440](https://peps.python.org/pep-0440/) +and [Semantic Versioning](https://semver.org/) to describe how the version +should change depending on the updates to the code base. [](){releasing-reference} ## Releasing @@ -67,19 +55,20 @@ See the pdm-bump docs for the The steps required are the following: - 1. Bump the version: manually trigger the "bump" workflow from the main branch - (see here: [bump workflow](https://github.com/openscm/openscm-zenodo/actions/workflows/bump.yaml)). - A valid "bump_rule" (see [pdm-bump's docs](https://github.com/carstencodes/pdm-bump#usage)) will need to be specified. + (see here: [bump workflow](https://github.com/openscm/OpenSCM-zenodo/actions/workflows/bump.yaml)). + A valid "bump_rule" (see [pdm-bump's docs](https://github.com/carstencodes/pdm-bump#usage)) + will need to be specified. This will then trigger a draft release. 1. Edit the draft release which has been created (see here: - [project releases](https://github.com/openscm/openscm-zenodo/releases)). - Once you are happy with the release (removed placeholders, added key - announcements etc.) then hit 'Publish release'. This triggers a release to - PyPI (which you can then add to the release if you want). - + [project releases](https://github.com/openscm/OpenSCM-zenodo/releases)). + Once you are happy with the release + (removed placeholders, added key announcements etc.) + then hit 'Publish release'. + This triggers a release to PyPI + (which you can then add to the release if you want). 1. That's it, release done, make noise on social media of choice, do whatever else @@ -88,9 +77,9 @@ The steps required are the following: ## Read the Docs -Our documentation is hosted by -[Read the Docs (RtD)](https://www.readthedocs.org/), a service for which we are -very grateful. The RtD configuration can be found in the `.readthedocs.yaml` -file in the root of this repository. The docs are automatically -deployed at +Our documentation is hosted by [Read the Docs (RtD)](https://www.readthedocs.org/), +a service for which we are very grateful. +The RtD configuration can be found in the `.readthedocs.yaml` file +in the root of this repository. +The docs are automatically deployed at [openscm-zenodo.readthedocs.io](https://openscm-zenodo.readthedocs.io/en/latest/). diff --git a/docs/explanation.md b/docs/further-background/index.md similarity index 95% rename from docs/explanation.md rename to docs/further-background/index.md index 9da03cb..3a766ee 100644 --- a/docs/explanation.md +++ b/docs/further-background/index.md @@ -1,3 +1,5 @@ +# Further background + This part of the project documentation will focus on an **understanding-oriented** approach. Here, we will describe the background of the project, diff --git a/docs/gen_doc_stubs.py b/docs/gen_doc_stubs.py index 125e5d5..851c3c5 100644 --- a/docs/gen_doc_stubs.py +++ b/docs/gen_doc_stubs.py @@ -1,7 +1,8 @@ """ Generate virtual doc files for the mkdocs site. -This script can also be run directly to actually write out those files, as a preview. +This script can also be run directly to actually write out those files, +as a preview. All credit to the creators of: https://oprypin.github.io/mkdocs-gen-files/ @@ -21,7 +22,7 @@ ROOT_DIR = Path("api") PACKAGE_NAME_ROOT = "openscm_zenodo" -TITLE_RENAMINGS = {"cli": "CLI", "openscm_zenodo": "openscm_zenodo"} +nav = mkdocs_gen_files.Nav() @define @@ -48,16 +49,13 @@ def write_subpackage_pages(package: object) -> tuple[PackageInfo, ...]: return tuple(sub_packages) -def get_write_file(package_full_name: str, title: str) -> Path: +def get_write_file(package_full_name: str) -> Path: """Get directory in which to write the doc file""" write_dir = ROOT_DIR for sub_dir in package_full_name.split(".")[:-1]: - if sub_dir in TITLE_RENAMINGS: - write_dir = write_dir / TITLE_RENAMINGS[sub_dir] - else: - write_dir = write_dir / sub_dir + write_dir = write_dir / sub_dir - write_file = write_dir / title / "index.md" + write_file = write_dir / package_full_name.split(".")[-1] / "index.md" return write_file @@ -108,15 +106,15 @@ def write_module_page( sub_packages = None package_name = package_full_name.split(".")[-1] - try: - title = TITLE_RENAMINGS[package_name] - except KeyError: - title = package_name.title() - write_file = get_write_file(package_full_name, title) + write_file = get_write_file(package_full_name) + + nav[package_full_name.split(".")] = write_file.relative_to( + ROOT_DIR / PACKAGE_NAME_ROOT + ).as_posix() with mkdocs_gen_files.open(write_file, "w") as fh: - fh.write(f"# {title}\n") + fh.write(f"# {package_full_name}\n") if sub_packages: fh.write("\n") @@ -135,3 +133,5 @@ def write_module_page( write_module_page(PACKAGE_NAME_ROOT) +with mkdocs_gen_files.open(ROOT_DIR / PACKAGE_NAME_ROOT / "NAVIGATION.md", "w") as fh: + fh.writelines(nav.build_literate_nav()) diff --git a/docs/how-to-guides/index.md b/docs/how-to-guides/index.md new file mode 100644 index 0000000..ea58c94 --- /dev/null +++ b/docs/how-to-guides/index.md @@ -0,0 +1,5 @@ +# How-to guides + +This part of the project documentation +focuses on a **problem-oriented** approach. +We'll go over how to solve common tasks. diff --git a/docs/installation.md b/docs/installation.md index 52af916..e43566f 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -1,15 +1,16 @@ # Installation -There are a few different ways to install openscm-zenodo. +There are a few different ways to install OpenSCM Zenodo. We provide these by use case below. As a short summary, if you: -- just want to use openscm-zenodo for validation, +- just want to use OpenSCM Zenodo for validation, and nothing else, go to [installation as an application][as-an-application] -- want to use openscm-zenodo's functionality +- want to use OpenSCM Zenodo's functionality as a library within another application, go to [installation as a library][as-a-library] -- want to develop openscm-zenodo, go to [installation for developers][for-developers] +- want to develop OpenSCM Zenodo, + go to [installation for developers][for-developers] ## By use case diff --git a/docs/tutorials.md b/docs/tutorials/index.md similarity index 97% rename from docs/tutorials.md rename to docs/tutorials/index.md index b92c6d9..21c69bb 100644 --- a/docs/tutorials.md +++ b/docs/tutorials/index.md @@ -1,3 +1,5 @@ +# Tutorials + This part of the project documentation will focus on a **learning-oriented** approach. You'll learn how to get started with the code in this project. diff --git a/mkdocs.yml b/mkdocs.yml index ae6de01..27398f6 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,29 +1,10 @@ -site_name: OpenSCM-Zenodo -site_description: Basic tools for interaction with Zenodo -site_url: https://openscm-zenodo.readthedocs.io/en/latest/ -edit_uri: blob/main/docs/ +site_name: OpenSCM Zenodo +site_description: Command-line tool for uploading to zenodo. +site_url: https://openscm-zenodo.readthedocs.io +edit_uri: blob/master/docs/ -repo_name: openscm/openscm-zenodo -repo_url: https://github.com/openscm/openscm-zenodo - -nav: - - OpenSCM-Zenodo: index.md - - Installation: installation.md - # TODO: write these - # - How-to guides: - # - how-to-guides/index.md - # - How to write a single valid file: how-to-guides/how-to-write-a-single-valid-file.py - # - How validate a single file: how-to-guides/how-to-validate-a-single-file.py - # - How to write a single file in the DRS: how-to-guides/how-to-write-a-single-file-in-the-drs.py - # - How to upload to an FTP server: how-to-guides/how-to-upload-to-ftp.py - # - How to manage a database of file entries: how-to-guides/how-to-manage-a-database.py - - Tutorials: tutorials.md - - Further background: - - Explanation: explanation.md - - Command-line interface: cli/index.md - - API reference: api/openscm_zenodo/ - - Development: development.md - - Changelog: changelog.md +repo_name: openscm/OpenSCM-zenodo +repo_url: https://github.com/openscm/OpenSCM-zenodo theme: name: "material" @@ -32,8 +13,10 @@ theme: palette: # Light mode (toggle to dark mode) - scheme: default + # Other colour choices at https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/#color-palette primary: blue - accent: deep orange + accent: orange + # More info on toggles at https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/#color-palette-toggle toggle: icon: material/weather-night name: Switch to dark mode @@ -47,72 +30,104 @@ theme: name: Switch to light mode plugins: - # Required for auto-generating our documentation stubs, - # a bit like sphinx autodoc gen used to do + # https://mkdocstrings.github.io/autorefs/ + - autorefs + # Required for auto-generating our documentation stubs + # https://oprypin.github.io/mkdocs-gen-files/ - gen-files: scripts: - docs/gen_doc_stubs.py - - search - - autorefs + # Make the navigation easier to handle/auto-generate if we wish + # https://oprypin.github.io/mkdocs-literate-nav/ + - literate-nav: + nav_file: NAVIGATION.md + # Notebook support. + # Working out how to make this play with nb-exec would be nice, + # then it wouldn't run every time. + # See also: https://github.com/danielfrg/mkdocs-jupyter/issues/161 + # We could also get the nb-exec-table mentioned here: + # https://myst-nb.readthedocs.io/en/v0.12.2/use/execute.html + # One for another day. + - mkdocs-jupyter: + # Use filenames for titles + ignore_h1_titles: True + include: ["*.py"] + execute: true + # Toggle off for faster builds + # execute: false + allow_errors: false + # theme: dark + include_source: True + ignore: ["*.ipynb", "*.md", "docs/gen_doc_stubs.py"] + remove_tag_config: + remove_input_tags: + - remove_input + # Docstring generation - mkdocstrings: enable_inventory: true handlers: python: paths: [src] import: - - https://www.attrs.org/en/latest/objects.inv + # Cross-ref helpers (lots included here, remove what you don't want) + - https://www.attrs.org/en/stable/objects.inv - https://unidata.github.io/cftime/objects.inv - - https://ncdata.readthedocs.io/en/latest/objects.inv - - https://pint.readthedocs.io/en/latest/objects.inv + - https://ipython.readthedocs.io/en/stable/objects.inv + - https://loguru.readthedocs.io/en/latest/objects.inv + - https://matplotlib.org/stable/objects.inv + - https://ncdata.readthedocs.io/en/stable/objects.inv + - https://openscm-units.readthedocs.io/en/stable/objects.inv + - https://pandas.pydata.org/docs/objects.inv + - https://pint.readthedocs.io/en/stable/objects.inv - https://www.fatiando.org/pooch/latest/objects.inv - https://docs.python.org/3/objects.inv - - https://scitools-iris.readthedocs.io/en/latest/objects.inv - - https://validators.readthedocs.io/en/latest/objects.inv - - http://xarray.pydata.org/en/latest/objects.inv - - https://loguru.readthedocs.io/en/latest/objects.inv + - https://docs.scipy.org/doc/scipy/objects.inv + - https://scitools-iris.readthedocs.io/en/stable/objects.inv + - https://scmdata.readthedocs.io/en/stable/objects.inv + - https://validators.readthedocs.io/en/stable/objects.inv + - http://xarray.pydata.org/en/stable/objects.inv options: docstring_style: numpy show_root_heading: true show_source: true - # # Make the nav recursive - - literate-nav - # nav_file: SUMMARY.md + # https://squidfunk.github.io/mkdocs-material/plugins/search/ + - search + # Add clickable sections to the sidebar # https://oprypin.github.io/mkdocs-section-index/ - # This won't work properly until we write a nav file too, job for another day - section-index - # Working out how to make this play with nb-exec would be nice, - # then it wouldn't run every time. - # We could also get the nb-exec-table mentioned here: - # https://myst-nb.readthedocs.io/en/v0.12.2/use/execute.html - # One for another day. - - mkdocs-jupyter: - execute: true - # execute: false - allow_errors: false - # theme: dark - include_source: True - ignore: ["*.ipynb", "docs/gen_doc_stubs.py"] - remove_tag_config: - remove_input_tags: - - remove_input markdown_extensions: + # https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#attribute-lists - attr_list + # Allow admonitions, useful for deprecation warnings + # https://facelessuser.github.io/pymdown-extensions/extensions/blocks/plugins/admonition/ + - pymdownx.blocks.admonition # Code highlighting handiness + # https://facelessuser.github.io/pymdown-extensions/extensions/highlight/ - pymdownx.highlight: anchor_linenums: true line_spans: __span pygments_lang_class: true + # https://facelessuser.github.io/pymdown-extensions/extensions/inlinehilite/ - pymdownx.inlinehilite + # Enable the use of snippets (e.g. taking snippets from README and putting them in docs) + # https://facelessuser.github.io/pymdown-extensions/extensions/snippets/ - pymdownx.snippets + # Support more complicated indents etc. + # https://facelessuser.github.io/pymdown-extensions/extensions/superfences/ - pymdownx.superfences + # Tabbed sections (e.g. for our installation options) + # https://facelessuser.github.io/pymdown-extensions/extensions/tabbed/ - pymdownx.tabbed: alternate_style: true + # Support tables (used in our API docs) + # https://squidfunk.github.io/mkdocs-material/reference/data-tables/ - tables # Ensure that there are links to table of contents items - toc: permalink: "#" watch: - - src - README.md + # Auto-generate if `src` changes (because this changes API docs) + - src diff --git a/pdm.lock b/pdm.lock index 21815ca..5c97513 100644 --- a/pdm.lock +++ b/pdm.lock @@ -2,20 +2,20 @@ # It is not intended for manual editing. [metadata] -groups = ["default", "dev", "docs", "notebooks", "tests"] +groups = ["default", "dev", "docs", "tests"] strategy = ["inherit_metadata"] lock_version = "4.5.0" -content_hash = "sha256:c5241e613ba7fb87cd5184e9c923a9068317117151e5f287fafc3a1c8bb6367f" +content_hash = "sha256:17412b24104af707c333e41684d6e7a24e82288934fb82d008e98e7a285cc74d" [[metadata.targets]] requires_python = ">=3.9" [[package]] name = "anyio" -version = "4.4.0" -requires_python = ">=3.8" +version = "4.6.0" +requires_python = ">=3.9" summary = "High level compatibility layer for multiple asynchronous event loop implementations" -groups = ["docs", "notebooks"] +groups = ["docs"] dependencies = [ "exceptiongroup>=1.0.2; python_version < \"3.11\"", "idna>=2.8", @@ -23,8 +23,8 @@ dependencies = [ "typing-extensions>=4.1; python_version < \"3.11\"", ] files = [ - {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"}, - {file = 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">=3.9" +dependencies = [ + "requests", + "tqdm", + "typer", + "loguru", + "attrs", +] +readme = "README.md" +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Developers", + "License :: OSI Approved :: BSD License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", +] +keyords = ["openscm", "zenodo", "command-line"] + +[project.optional-dependencies] + +[build-system] +requires = [ + "pdm-backend", + "pdm-build-locked", +] +build-backend = "pdm.backend" +[tool.pdm] [tool.pdm.build] locked = true includes = [ @@ -8,6 +44,41 @@ includes = [ "LICENCE", ] +[tool.pdm.dev-dependencies] +dev = [ + "pre-commit>=3.8.0", + "mypy>=1.11", + "towncrier>=24.8.0", + "liccheck>=0.9.2", + # Required for liccheck + "setuptools>=74.1.2", + "pip>=24.2", + "types-tqdm>=4.66.0.20240417", + "types-requests>=2.32.0.20240712", +] +docs = [ + "attrs>=24.0.0", + 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"⚠️ Breaking Changes", showcontent = true }, { directory = "deprecation", name = "🗑️ Deprecations", showcontent = true }, @@ -155,85 +226,3 @@ unauthorized_licenses = [ "gpl v1", "gplv1", ] - -[project] -name = "openscm-zenodo" -version = "0.3.1a1" -description = "Command-line tool for uploading to zenodo" -keywords = [ - "zenodo", - "command-line", -] -readme = "README.md" -authors = [ - { name = "Zebedee Nicholls", email = "zebedee.nicholls@climate-energy-college.org" }, - { name = "Jared Lewis", email = "jared.lewis@climate-energy-college.org" }, -] -classifiers = [ - "Development Status :: 4 - Beta", - "Intended Audience :: Developers", - "License :: OSI Approved :: BSD License", - "Operating System :: OS Independent", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", -] -dependencies = [ - "requests", - "tqdm", - "typer", - "loguru", - "attrs", -] -requires-python = ">=3.9" - -[project.license] -text = "3-Clause BSD License" - -[project.urls] -Homepage = "https://github.com/openscm/openscm-zenodo" -"Bug Reports" = "https://github.com/openscm/openscm-zenodo/issues" -Documentation = "https://openscm-zenodo.readthedocs.io/" -Source = "https://github.com/openscm/openscm-zenodo" - -[project.optional-dependencies] -dev = [ - "mypy>=1.11.1", - "pre-commit>=3.8.0", - "types-tqdm>=4.66.0.20240417", - "types-requests>=2.32.0.20240712", - "towncrier>=23.11.0,<24", - "liccheck>=0.9.2", - "pip>=24.2", - "websocket-client>=1.8.0", -] -docs = [ - "mkdocs>=1.6.0", - "mkdocs-material>=9.5.32", - "mkdocstrings[python]>=0.25.2", - "mkdocs-gen-files>=0.5.0", - "mkdocs-literate-nav>=0.6.1", - "mkdocs-section-index>=0.3.9", - "mkdocs-autorefs>=1.0.1", - "mkdocs-jupyter>=0.24.8", - "jupyterlab>=4.2.4", - "jupytext>=1.16.4", -] -notebooks = [ - "jupyterlab>=4.2.4", -] -tests = [ - "pytest>=8.3.2", - "coverage>=7.6.1", - "pytest-cov>=5.0.0", -] - -[project.scripts] -openscm-zenodo = "openscm_zenodo.cli:app" - -[build-system] -requires = [ - "pdm-backend", - "pdm-build-locked", -] -build-backend = "pdm.backend" diff --git a/requirements-docs-locked.txt b/requirements-docs-locked.txt new file mode 100644 index 0000000..a6e52de --- /dev/null +++ b/requirements-docs-locked.txt @@ -0,0 +1,135 @@ +# This file is @generated by PDM. +# Please do not edit it manually. + +anyio==4.6.0 +appnope==0.1.4; platform_system == "Darwin" +argon2-cffi==23.1.0 +argon2-cffi-bindings==21.2.0 +arrow==1.3.0 +asttokens==2.4.1 +async-lru==2.0.4 +attrs==24.2.0 +babel==2.16.0 +beautifulsoup4==4.12.3 +bleach==6.1.0 +certifi==2024.8.30 +cffi==1.17.1 +charset-normalizer==3.3.2 +click==8.1.7 +colorama==0.4.6 +comm==0.2.2 +debugpy==1.8.6 +decorator==5.1.1 +defusedxml==0.7.1 +exceptiongroup==1.2.2; python_version < "3.11" +executing==2.1.0 +fastjsonschema==2.20.0 +fqdn==1.5.1 +ghp-import==2.1.0 +griffe==1.3.1 +h11==0.14.0 +httpcore==1.0.5 +httpx==0.27.2 +idna==3.10 +importlib-metadata==8.5.0; python_version < "3.10" +ipykernel==6.29.5 +ipython==8.18.1 +isoduration==20.11.0 +jedi==0.19.1 +jinja2==3.1.4 +json5==0.9.25 +jsonpointer==3.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +jsonschema[format-nongpl]==4.23.0 +jupyter-client==8.6.3 +jupyter-core==5.7.2 +jupyter-events==0.10.0 +jupyter-lsp==2.2.5 +jupyter-server==2.14.2 +jupyter-server-terminals==0.5.3 +jupyterlab==4.2.5 +jupyterlab-pygments==0.3.0 +jupyterlab-server==2.27.3 +jupytext==1.16.4 +loguru==0.7.2 +markdown==3.7 +markdown-it-py==3.0.0 +markupsafe==2.1.5 +matplotlib-inline==0.1.7 +mdit-py-plugins==0.4.2 +mdurl==0.1.2 +mergedeep==1.3.4 +mistune==3.0.2 +mkdocs==1.6.1 +mkdocs-autorefs==1.2.0 +mkdocs-gen-files==0.5.0 +mkdocs-get-deps==0.2.0 +mkdocs-jupyter==0.25.0 +mkdocs-literate-nav==0.6.1 +mkdocs-material==9.5.38 +mkdocs-material-extensions==1.3.1 +mkdocs-section-index==0.3.9 +mkdocstrings==0.26.1 +mkdocstrings-python==1.11.1 +mkdocstrings[python]==0.26.1 +nbclient==0.10.0 +nbconvert==7.16.4 +nbformat==5.10.4 +nest-asyncio==1.6.0 +notebook-shim==0.2.4 +overrides==7.7.0 +packaging==24.1 +paginate==0.5.7 +pandocfilters==1.5.1 +parso==0.8.4 +pathspec==0.12.1 +pexpect==4.9.0; sys_platform != "win32" +platformdirs==4.3.6 +prometheus-client==0.21.0 +prompt-toolkit==3.0.48 +psutil==6.0.0 +ptyprocess==0.7.0; os_name != "nt" or sys_platform != "win32" +pure-eval==0.2.3 +pycparser==2.22 +pygments==2.18.0 +pymdown-extensions==10.10.2 +python-dateutil==2.9.0.post0 +python-json-logger==2.0.7 +pywin32==306; sys_platform == "win32" and platform_python_implementation != "PyPy" +pywinpty==2.0.13; os_name == "nt" +pyyaml==6.0.2 +pyyaml-env-tag==0.1 +pyzmq==26.2.0 +referencing==0.35.1 +regex==2024.9.11 +requests==2.32.3 +rfc3339-validator==0.1.4 +rfc3986-validator==0.1.1 +rich==13.8.1 +rpds-py==0.20.0 +send2trash==1.8.3 +setuptools==75.1.0 +shellingham==1.5.4 +six==1.16.0 +sniffio==1.3.1 +soupsieve==2.6 +stack-data==0.6.3 +terminado==0.18.1 +tinycss2==1.3.0 +tomli==2.0.1; python_version < "3.11" +tornado==6.4.1 +tqdm==4.66.5 +traitlets==5.14.3 +typer==0.12.5 +types-python-dateutil==2.9.0.20240906 +typing-extensions==4.12.2 +uri-template==1.3.0 +urllib3==2.2.3 +watchdog==5.0.2 +wcwidth==0.2.13 +webcolors==24.8.0 +webencodings==0.5.1 +websocket-client==1.8.0 +win32-setctime==1.1.0; sys_platform == "win32" +zipp==3.20.2; python_version < "3.10" diff --git a/requirements.txt b/requirements-locked.txt similarity index 81% rename from requirements.txt rename to requirements-locked.txt index ab26ebb..5367182 100644 --- a/requirements.txt +++ b/requirements-locked.txt @@ -2,20 +2,20 @@ # Please do not edit it manually. attrs==24.2.0 -certifi==2024.7.4 +certifi==2024.8.30 charset-normalizer==3.3.2 click==8.1.7 colorama==0.4.6 -idna==3.7 +idna==3.10 loguru==0.7.2 markdown-it-py==3.0.0 mdurl==0.1.2 pygments==2.18.0 requests==2.32.3 -rich==13.7.1 +rich==13.8.1 shellingham==1.5.4 tqdm==4.66.5 -typer==0.12.4 +typer==0.12.5 typing-extensions==4.12.2 -urllib3==2.2.2 +urllib3==2.2.3 win32-setctime==1.1.0; sys_platform == "win32" diff --git a/scripts/changelog-to-release-template.py b/scripts/changelog-to-release-template.py index 348812b..ce10241 100644 --- a/scripts/changelog-to-release-template.py +++ b/scripts/changelog-to-release-template.py @@ -33,14 +33,14 @@ def main() -> None: continue if not grab_notes: - if line.startswith("## OpenSCM-Zenodo"): + if line.startswith("## OpenSCM Zenodo"): grab_notes = True continue # We are grabbing notes now # If we've reached the next version's notes, break - if line.startswith("## OpenSCM-Zenodo"): + if line.startswith("## OpenSCM Zenodo"): break latest_version_notes.append(line) diff --git a/src/openscm_zenodo/zenodo.py b/src/openscm_zenodo/zenodo.py index 20deb2c..71d8832 100644 --- a/src/openscm_zenodo/zenodo.py +++ b/src/openscm_zenodo/zenodo.py @@ -940,7 +940,7 @@ def retrieve_bibtex_entry( doi = {10.5281/zenodo.4589756}, url = {https://doi.org/10.5281/zenodo.4589756} } - """ # noqa: #E501 + """ if zenoodo_interactor is None: zenoodo_interactor = ZenodoInteractor() diff --git a/stubs/.gitkeep b/stubs/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/tests/integration/.gitkeep b/tests/integration/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/tests/integration/test_cli_integration.py b/tests/integration/test_cli_integration.py new file mode 100644 index 0000000..90f24ed --- /dev/null +++ b/tests/integration/test_cli_integration.py @@ -0,0 +1,19 @@ +""" +Integration tests of the CLI +""" + +from __future__ import annotations + +from typer.testing import CliRunner + +import openscm_zenodo +from openscm_zenodo.cli import app + +runner = CliRunner() + + +def test_version(): + result = runner.invoke(app, ["--version"]) + + assert result.exit_code == 0, result.exc_info + assert result.stdout == f"openscm-zenodo {openscm_zenodo.__version__}\n" diff --git a/tests/regression/.gitkeep b/tests/regression/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/tests/test-data/.gitkeep b/tests/test-data/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/tests/unit/.gitkeep b/tests/unit/.gitkeep new file mode 100644 index 0000000..e69de29