diff --git a/.github/ISSUE_TEMPLATE/bug-report.yml b/.github/ISSUE_TEMPLATE/bug-report.yml new file mode 100644 index 00000000..5cc57829 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug-report.yml @@ -0,0 +1,149 @@ +--- +name: 🐛 Bug Report +description: Create a report to help us improve +labels: ["bug", "needs-triage"] + +body: + - type: markdown + attributes: + value: > + **Thank you for wanting to report a bug in PyMedX!** + + + ⚠ + Verify first that your issue is not [already reported on + GitHub][issue search]. + + + [issue search]: https://github.com/PyMedX/issues?q=is%3Aopen+is%3Aissue+label%3Abug + + - type: textarea + attributes: + label: Summary + description: Explain the problem briefly below. + placeholder: >- + When I try to do X with {{ cookiecutter.project_name }} and the following workspace, Y breaks or + Z happens in an unexpected manner. + Here are all the details I know about this problem. + validations: + required: true + + - type: textarea + attributes: + label: OS / Environment + description: >- + Provide information on your operating system. + Something like the output of `cat /etc/os-release` on Linux or + `system_profiler -detailLevel mini SPSoftwareDataType` on macOS. + render: console + placeholder: | + # Linux + $ cat /etc/os-release + NAME="Ubuntu" + VERSION="20.04.2 LTS (Focal Fossa)" + ID=ubuntu + ID_LIKE=debian + PRETTY_NAME="Ubuntu 20.04.2 LTS" + VERSION_ID="20.04" + HOME_URL="https://www.ubuntu.com/" + SUPPORT_URL="https://help.ubuntu.com/" + BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/" + PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy" + VERSION_CODENAME=focal + UBUNTU_CODENAME=focal + + # macOS + $ system_profiler -detailLevel mini SPSoftwareDataType | head -n 6 + Software: + + System Software Overview: + + System Version: macOS 10.15.7 (19H1323) + Kernel Version: Darwin 19.6.0 + validations: + required: true + + - type: textarea + attributes: + label: Steps to Reproduce + description: >- + Describe exactly how to reproduce the problem, using a minimal test-case. + It would *really* help us understand your problem if you paste in the Python code + that you're running. + + + **HINT:** You can paste [GitHub Gist](https://gist.github.com) links for larger files. + value: | + + ```python (paste below) + + ``` + + + ```console (paste below) + + ``` + validations: + required: true + + - type: textarea + attributes: + label: File Upload (optional) + description: >- + If your steps to reproduce your minimal failing example require either a spec or a + workspace file, please upload it by attaching it to the text area here. + + + **HINT:** You can paste [GitHub Gist](https://gist.github.com) links for larger files. + placeholder: >- + Attach any files or compressed archives by dragging & dropping, selecting, + or pasting them here. + validations: + required: false + + - type: textarea + attributes: + label: Expected Results + description: >- + Describe what you expected to happen when running the steps above. + placeholder: >- + I expected X to happen because I assumed Y. + validations: + required: true + + - type: textarea + attributes: + label: Actual Results + description: >- + Paste verbatim program or command output. + Don't wrap it with triple backticks — your whole input will be + turned into a code snippet automatically. + render: console + validations: + required: true + + - type: textarea + attributes: + # label: PyMedX version + # description: >- + # Paste verbatim output from `PyMedX --version` below, under the prompt line. + # Don't wrap it with triple backticks — your whole input will be + # turned into a code snippet automatically. + render: console + placeholder: | + python -m pip show PyMedX + validations: + required: true + + - type: checkboxes + attributes: + label: Code of Conduct + description: | + Read the [`PyMedX` Code of Conduct][CoC] first. + + [CoC]: https://github.com/osl-incubator/pymedx/coc/CODE_OF_CONDUCT.md + options: + - label: I agree to follow the Code of Conduct + required: true +--- +This template has been adopted from [pyhf](https://github.com/scikit-hep/pyhf/tree/main/.github/ISSUE_TEMPLATE)'s excellent bug report template. diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 00000000..1b30aad9 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,15 @@ +# Ref: https://help.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository#configuring-the-template-chooser +blank_issues_enabled: true +contact_links: + - name: 🙋 Usage Questions + url: https://github.com/osl-incubator/pymedx/discussions + about: | + Use PyMedX's GitHub Discussions to ask "How do I do X with Cookiecutter?". + - name: 📖 Tutorial + url: https://github.com/osl-incubator/pymedx + about: | + The PyMedX tutorial is continually updated and provides an in depth walkthrough + of how to use the latest release of Cookiecutter. + - name: 📝 PyMedX Code of Conduct + url: https://github.com/osl-incubator/pymedx/coc/CODE_OF_CONDUCT.md + about: Expectations for how people will interact with each other on Cookiecutter's GitHub. diff --git a/.github/ISSUE_TEMPLATE/documentation-report.yml b/.github/ISSUE_TEMPLATE/documentation-report.yml new file mode 100644 index 00000000..1b59b15c --- /dev/null +++ b/.github/ISSUE_TEMPLATE/documentation-report.yml @@ -0,0 +1,53 @@ +--- +name: 📝 Documentation Report +description: Create a report for problems with the docs +labels: ["docs", "needs-triage"] + +body: + - type: markdown + attributes: + value: > + **Thank you for wanting to report a problem with PyMedX's documentation!** + + + ⚠ + Verify first that your issue is not [already reported on + GitHub][issue search]. + + + [issue search]: https://github.com/PyMedX/issues?q=is%3Aopen+is%3Aissue+label%3Adocs + + - type: textarea + attributes: + label: Summary + description: >- + Explain the problem briefly below, add suggestions to wording or structure. + If there are external references that are related please link them here + as well. + placeholder: >- + I was reading the PyMedX documentation for PyMedX version X and I'm having + problems understanding Y. + It would be very helpful if that got rephrased as Z. + validations: + required: true + + - type: input + attributes: + label: Documentation Page Link + description: | + Paste the link to the documentation webpage that you have a question on. + validations: + required: true + + - type: checkboxes + attributes: + label: Code of Conduct + description: | + Read the [`PyMedX` Code of Conduct][CoC] first. + + [CoC]: https://github.com/PyMedX/blob/main/CODE_OF_CONDUCT.md + options: + - label: I agree to follow the Code of Conduct + required: true +--- +This template has been adopted from [pyhf](https://github.com/scikit-hep/pyhf/tree/main/.github/ISSUE_TEMPLATE)'s excellent bug report template. diff --git a/.github/ISSUE_TEMPLATE/feature-request.yml b/.github/ISSUE_TEMPLATE/feature-request.yml new file mode 100644 index 00000000..8a428f81 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature-request.yml @@ -0,0 +1,80 @@ +--- +name: ✨ Feature Request +description: Suggest an idea for this project +labels: ["feat/enhancement ", "needs-triage"] + +body: + - type: markdown + attributes: + value: > + **Thank you for wanting to suggest a feature for PyMedX!** + + + ⚠ + Verify first that your issue is not [already reported on + GitHub][issue search]. + Make sure to check the closed issues as well as it may + already be implemented in a development release. + + + [issue search]: https://github.com/PyMedX/issues?q=is%3Aopen+is%3Aissue+label%3Afeat%2Fenhancement + + - type: textarea + attributes: + label: Summary + description: > + Describe the new feature/improvement you would like briefly below. + + + What's the problem this feature will solve? + What are you trying to do, that you are unable to achieve + with the **latest** release of Cookiecutter? + + + * Provide examples of real-world use cases that this would enable + and how it solves the problem you described. + + * How do you solve this now? + + * Have you tried to work around the problem? + + * Could there be a different approach to solving this issue? + + + If there are external references or other GitHub Issues that are related + please link them here as well. + placeholder: >- + I am trying to do X with PyMedX version x.y.z and I think that implementing + new feature Y would be very helpful for me and every other user because of Z. + validations: + required: true + + - type: textarea + attributes: + label: Additional Information + description: | + If you can, describe how the feature would be used in a mock code example. + + **HINT:** You can paste [GitHub Gist](https://gist.github.com) links for larger files. + value: | + + + + ```python (paste below) + + ``` + validations: + required: false + + - type: checkboxes + attributes: + label: Code of Conduct + description: | + Read the [`PyMedX` Code of Conduct][CoC] first. + + [CoC]: https://github.com/osl-incubator/pymedx/coc/CODE_OF_CONDUCT.md + options: + - label: I agree to follow the Code of Conduct + required: true +--- +This template has been adopted from [pyhf](https://github.com/scikit-hep/pyhf/tree/main/.github/ISSUE_TEMPLATE)'s excellent bug report template. diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml new file mode 100644 index 00000000..621c4afc --- /dev/null +++ b/.github/workflows/main.yaml @@ -0,0 +1,116 @@ +name: main + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + check-branch: + if: ${{ github.event_name == 'pull_request' }} + runs-on: ubuntu-latest + timeout-minutes: 10 + concurrency: + group: check-pr-${{ github.ref }} + cancel-in-progress: true + + steps: + - uses: actions/checkout@v3 + with: + fetch-depth: 0 + + - name: Check if the PR's branch is updated + uses: osl-incubator/gh-check-pr-is-updated@1.0.0 + with: + remote_branch: origin/main + pr_sha: ${{ github.event.pull_request.head.sha }} + + tests: + needs: check-branch + strategy: + matrix: + python_version: + - "3.8.1" + - "3.9" + - "3.10" + - "3.11" + # - '3.12' + os: + - "ubuntu" + # - 'macos' + # poetry is failing on windows: https://github.com/python-poetry/poetry/issues/1031 + # - 'windows' + + runs-on: ${{ matrix.os }}-latest + timeout-minutes: 10 + concurrency: + group: ci-tests-${{ matrix.os }}-${{ matrix.python_version }}-${{ github.ref }} + cancel-in-progress: true + + defaults: + run: + shell: bash -l {0} + + steps: + - uses: actions/checkout@v3 + + - uses: conda-incubator/setup-miniconda@v3 + with: + miniconda-version: "latest" + environment-file: conda/dev.yaml + channels: conda-forge,nodefaults + activate-environment: pymedx + auto-update-conda: true + conda-solver: libmamba + + - name: Install dependencies + run: | + sudo apt install ffmpeg + poetry install + + - name: Run tests + run: makim tests.unittest + + linter-and-docs: + needs: check-branch + runs-on: ubuntu-latest + timeout-minutes: 10 + + defaults: + run: + shell: bash -l {0} + + concurrency: + group: ci-linter-docs-${{ matrix.os }}-${{ matrix.python_version }}-${{ github.ref }} + cancel-in-progress: true + + steps: + - uses: actions/checkout@v3 + + - uses: conda-incubator/setup-miniconda@v3 + with: + miniconda-version: "latest" + environment-file: conda/dev.yaml + channels: conda-forge,nodefaults + activate-environment: pymedx + auto-update-conda: true + conda-solver: libmamba + + - name: Install dependencies + run: | + poetry config virtualenvs.create false + poetry install + + - name: Test documentation generation + run: makim docs.build + + - name: Run style checks + if: success() || failure() + run: | + pre-commit install + makim tests.linter + + - name: Setup tmate session + if: "${{ failure() && (contains(github.event.pull_request.labels.*.name, 'ci:enable-debugging')) }}" + uses: mxschmitt/action-tmate@v3 diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml new file mode 100644 index 00000000..3129e3f5 --- /dev/null +++ b/.github/workflows/release.yaml @@ -0,0 +1,64 @@ +name: Release + +on: + workflow_dispatch: + push: + branches: [main] + pull_request: + branches: [main] + +permissions: + contents: write + issues: write + pull-requests: write + +jobs: + release: + name: Release + runs-on: ubuntu-latest + timeout-minutes: 10 + + defaults: + run: + shell: bash -l {0} + + steps: + - uses: actions/checkout@v3 + + - uses: conda-incubator/setup-miniconda@v2 + with: + miniconda-version: "latest" + mamba-version: "1.*" + environment-file: conda/dev.yaml + channels: conda-forge,nodefaults + activate-environment: pymedx + use-mamba: true + miniforge-variant: Mambaforge + + - name: Install deps + run: poetry install + + - name: Run semantic release (for tests) + if: ${{ github.event_name != 'workflow_dispatch' }} + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: makim release.dry + + - name: Release command + if: ${{ github.event_name == 'workflow_dispatch' }} + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} + run: | + poetry config pypi-token.pypi ${PYPI_TOKEN} + makim release.ci + + - name: Generate documentation with changes from semantic-release + run: makim docs.build + + - name: GitHub Pages action + if: ${{ github.event_name == 'workflow_dispatch' }} + uses: peaceiris/actions-gh-pages@v3.5.9 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: ./build diff --git a/.gitignore b/.gitignore index a8034706..8249fdbb 100644 --- a/.gitignore +++ b/.gitignore @@ -100,8 +100,9 @@ venv.bak/ # mkdocs documentation /site -# mypy +# tools .mypy_cache/ +.ruff_cache/ DSS.egg-info/ test-reports/ diff --git a/.makim.yaml b/.makim.yaml new file mode 100644 index 00000000..a5f03d3f --- /dev/null +++ b/.makim.yaml @@ -0,0 +1,82 @@ +version: 1.0 +groups: + clean: + targets: + all: + help: remove build artifacts, compiled files, and cache + shell: bash + run: | + find . -name '*.egg-info' -exec rm -rf {} + + find . -name '*.egg' -exec rm -f {} + + find . -name '*.pyc' -exec rm -f {} + + find . -name '*.pyo' -exec rm -f {} + + find . -name '__pycache__' -exec rm -rf {} + + find . -name '*~' -exec rm -f {} + + rm -rf build/ + rm -rf dist/ + rm -rf .eggs/ + rm -f .coverage + rm -rf htmlcov/ + rm -rf .pytest_cache + + tests: + targets: + linter: + help: run linter tools + run: | + pre-commit install + pre-commit run --all-files + + unittest: + help: run tests + args: + path: + help: Specify the location of the tests + type: string + default: "" + params: + help: Specify parameters to be used for tests + type: string + default: "-vv" + run: pytest {{ args.path }} {{ args.params }} + + ci: + help: run the sames tests executed on CI + dependencies: + - target: tests.unittest + - target: tests.linter + + docs: + targets: + build: + help: build documentation + run: | + mkdocs build --config-file mkdocs.yaml + + preview: + help: preview documentation page locally + run: mkdocs serve --watch docs --config-file mkdocs.yaml + + release: + vars: + app: | + npx --yes \ + -p semantic-release \ + -p conventional-changelog-conventionalcommits \ + -p "@semantic-release/commit-analyzer" \ + -p "@semantic-release/release-notes-generator" \ + -p "@semantic-release/changelog" \ + -p "@semantic-release/exec" \ + -p "@semantic-release/github" \ + -p "@semantic-release/git" \ + -p "@google/semantic-release-replace-plugin" \ + semantic-release + + targets: + ci: + help: run semantic release on CI + run: {{ vars.app }} --ci + + dry: + help: run semantic release in dry-run mode + run: {{ vars.app }} --dry-run diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..b37b22e8 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,95 @@ +default_stages: + - commit +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.1.0 + hooks: + - id: end-of-file-fixer + + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v3.0.2" + hooks: + - id: prettier + exclude: ".makim.yaml" + + - repo: local + hooks: + - id: ruff-format + name: ruff-format + entry: ruff format + exclude: | + (?x)( + docs + ) + language: system + pass_filenames: true + types: + - python + + - id: ruff-linter + name: ruff-linter + entry: ruff check + language: system + exclude: | + (?x)( + docs| + tests + ) + pass_filenames: true + types: + - python + + - id: mypy + name: mypy + entry: mypy + language: system + files: "./" + pass_filenames: true + exclude: | + (?x)( + docs| + tests + ) + types: + - python + + - id: shellcheck + name: shellcheck + entry: shellcheck + language: system + types_or: + - sh + - shell + - ash + - bash + - bats + - dash + - ksh + + - id: bandit + name: bandit + entry: bandit + language: system + args: ["--configfile", "pyproject.toml", "-iii", "-lll"] + pass_filenames: true + types: + - python + + - id: vulture + name: vulture + entry: vulture --min-confidence 80 + language: system + files: "src/umlizer" + description: Find unused Python code. + pass_filenames: true + types: + - python + + - id: mccabe + name: mccabe + entry: python -m mccabe --min 10 + language: system + files: "src/umlizer" + pass_filenames: true + types: + - python diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 00000000..66184464 --- /dev/null +++ b/.prettierignore @@ -0,0 +1,2 @@ +.makim.yaml +docs/changelog.md diff --git a/.prettierrc.yaml b/.prettierrc.yaml new file mode 100644 index 00000000..24d3b9f5 --- /dev/null +++ b/.prettierrc.yaml @@ -0,0 +1,6 @@ +overrides: + - files: "*.md" + options: + parser: remark + proseWrap: always + printWidth: 80 diff --git a/.releaserc.json b/.releaserc.json new file mode 100644 index 00000000..19d94fbe --- /dev/null +++ b/.releaserc.json @@ -0,0 +1,74 @@ +{ + "branches": ["main"], + "tagFormat": "${version}", + "plugins": [ + "@semantic-release/commit-analyzer", + [ + "@google/semantic-release-replace-plugin", + { + "replacements": [ + { + "files": ["src/pymedx/__init__.py"], + "from": "return \".*\" # semantic-release", + "to": "return \"${nextRelease.version}\" # semantic-release", + "results": [ + { + "file": "src/pymedx/__init__.py", + "hasChanged": true, + "numMatches": 1, + "numReplacements": 1 + } + ], + "countMatches": true + }, + { + "files": ["pyproject.toml"], + "from": "version = \".*\" # semantic-release", + "to": "version = \"${nextRelease.version}\" # semantic-release", + "results": [ + { + "file": "pyproject.toml", + "hasChanged": true, + "numMatches": 1, + "numReplacements": 1 + } + ], + "countMatches": true + } + ] + } + ], + "@semantic-release/release-notes-generator", + [ + "@semantic-release/changelog", + { + "changelogTitle": "# Release Notes\n---", + "changelogFile": "docs/changelog.md" + } + ], + [ + "@semantic-release/exec", + { + "prepareCmd": "poetry build", + "publishCmd": "poetry publish" + } + ], + [ + "@semantic-release/github", + { + "assets": ["dist/*.whl", "dist/*.tar.gz"] + } + ], + [ + "@semantic-release/git", + { + "assets": [ + "pyproject.toml", + "docs/changelog.md", + "src/pymedx/__init__.py" + ], + "message": "chore(release): ${nextRelease.version}" + } + ] + ] +} diff --git a/README.md b/README.md index 2bef0e0d..70e3dcfa 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -> PyMedX is a fork from a archived project called PyMed: https://github.com/gijswobben/pymed +> PyMedX is a fork from a archived project called PyMed: https://github.com/gijswobben/pymedx -# PyMed - PubMed Access through Python -PyMed is a Python library that provides access to PubMed through the PubMed API. +# PyMedX - PubMed Access through Python +PyMedX is a Python library that provides access to PubMed through the PubMed API. ## Why this library? The PubMed API is not very well documented and querying it in a performant way is too complicated and time consuming for researchers. This wrapper provides access to the API in a consistent, readable and performant way. @@ -17,7 +17,7 @@ This library takes care of the following for you: For full (working) examples have a look at the `examples/` folder in this repository. In essence you only need to import the `PubMed` class, instantiate it, and use it to query: ```python -from pymed import PubMed +from pymedx import PubMed pubmed = PubMed(tool="MyTool", email="my@email.address") results = pubmed.query("Some query", max_results=500) ``` @@ -30,5 +30,5 @@ The original documentation of the PubMed API can be found here: [PubMed Central] > * _tool_ should be the name of the application, as a string value with no internal spaces, and > * _email_ should be the e-mail address of the maintainer of the tool, and should be a valid e-mail address. -## Notice of Non-Affiliation and Disclaimer +## Notice of Non-Affiliation and Disclaimer The author of this library is not affiliated, associated, authorized, endorsed by, or in any way officially connected with PubMed, or any of its subsidiaries or its affiliates. The official PubMed website can be found at https://www.ncbi.nlm.nih.gov/pubmed/. diff --git a/_config.yml b/_config.yml deleted file mode 100644 index c7418817..00000000 --- a/_config.yml +++ /dev/null @@ -1 +0,0 @@ -theme: jekyll-theme-slate \ No newline at end of file diff --git a/build.py b/build.py deleted file mode 100644 index afaf8361..00000000 --- a/build.py +++ /dev/null @@ -1,111 +0,0 @@ -import os -import click -import shutil - -from git import Repo -from pymed.version import __version__ - - -def clean(): - """ Clean directories that are the result of a build. - """ - - # Loop over the directories that should be deleted - for directory in ["./build/", "./dist/", "./venv/"]: - try: - shutil.rmtree(os.path.abspath(directory)) - except FileNotFoundError as e: - pass - except Exception as e: - raise e - - -def buildPackage(username, password, production=False): - """ Method that builds a package and uploads it to PyPi. - """ - - # Make sure we have a clean slate - clean() - - # Run these OS commands to build and upload the package - os.system("python setup.py sdist bdist_wheel") - if production: - os.system(f"twine upload -u {username} -p {password} --repository pypiprd dist/*") - else: - os.system(f"twine upload -u {username} -p {password} --repository pypi dist/*") - - # Clean any mess we made - clean() - - -def commitChanges(): - """ Commit any new version file (created by an automatic bump). - """ - - # Get a reference to the Git repo (in this folder) - repo = Repo(os.path.dirname(__file__)) - - # Commit the new version - repo.git.commit("pymed/version.py", message="Bumped the release version") - - # Push any changes - repo.git.push("origin", "master") - - -def bumpVersion(release_type: str = "revision", direction: int = 1): - """ Bump the version number in the version file. - """ - - # Parse the current version - major, minor, revision = __version__.split(".") - - # Increase (or decrease) the number - if release_type == "major": - major = int(major) + direction - if release_type == "minor": - minor = int(minor) + direction - if release_type == "revision": - revision = int(revision) + direction - - # Assemble the new version number - new_version = f"{major}.{minor}.{revision}" - - # Open the version file and save the new version number - with open("pymed/version.py", "w") as version_file: - version_file.write(f"""__version__ = "{new_version}"\n""") - - # Return the new version - return new_version - - -@click.command() -@click.option("--username", "-u", help="Username to publish to PyPi") -@click.option("--password", "-p", help="Password for publishing to PyPi") -@click.option( - "--release_type", "-t", default="revision", help="Type of release to build" -) -@click.option("--production/--no-production", default=False) -def build(release_type, username, password, production): - """ Method that chains together the bumping of the version, committing the change and pushing the new package. - """ - - # Check the input - if release_type not in ["major", "minor", "revision"]: - raise Exception( - "Unknown release type, choose one of the following: 'major', 'minor', or 'revision'" - ) - - # Bump the version - new_version = bumpVersion(release_type=release_type) - print(f"Bumping the version. New version is: {new_version}") - - # Commit changes to Git - print("Commit and push changes to Git") - commitChanges() - - print("Build the package and upload it to PyPi") - buildPackage(username=username, password=password, production=production) - - -if __name__ == "__main__": - build() diff --git a/conda/dev.yaml b/conda/dev.yaml new file mode 100644 index 00000000..543352e7 --- /dev/null +++ b/conda/dev.yaml @@ -0,0 +1,12 @@ +name: pymedx +channels: + - nodefaults + - conda-forge +dependencies: + - python >=3.8.1,<4 + - pip + - poetry + - nodejs # used by semantic-release + - shellcheck + - pip: + - paginate diff --git a/docs/api/references.md b/docs/api/references.md new file mode 100644 index 00000000..eebb5b19 --- /dev/null +++ b/docs/api/references.md @@ -0,0 +1,3 @@ +# Api references + +::: pymedx diff --git a/docs/api/references.rst b/docs/api/references.rst new file mode 100644 index 00000000..bed482be --- /dev/null +++ b/docs/api/references.rst @@ -0,0 +1,8 @@ +API references +============== + +.. automodule:: pymedx + :members: + +.. automodule:: pymedx.pymedx + :members: diff --git a/docs/changelog.md b/docs/changelog.md new file mode 100644 index 00000000..254524bd --- /dev/null +++ b/docs/changelog.md @@ -0,0 +1,2 @@ +# Release Notes +--- diff --git a/docs/contributing.md b/docs/contributing.md new file mode 100644 index 00000000..feb7e8d0 --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1,161 @@ +# Contributing + +In order to be able to contribute, it is important that you understand the +project layout. This project uses the _src layout_, which means that the package +code is located at `./src/pymedx`. + +For my information, check the official documentation: +https://packaging.python.org/en/latest/discussions/src-layout-vs-flat-layout/ + +In addition, you should know that to build our package we use +[Poetry](https://python-poetry.org/), it's a Python package management tool that +simplifies the process of building and publishing Python packages. It allows us +to easily manage dependencies, virtual environments and package versions. Poetry +also includes features such as dependency resolution, lock files and publishing +to PyPI. Overall, Poetry streamlines the process of managing Python packages, +making it easier for us to create and share our code with others. + +Contributions are welcome, and they are greatly appreciated! Every little bit +helps, and credit will always be given. + +You can contribute in many ways: + +## Types of Contributions + +### Report Bugs + +Report bugs at https://github.com/osl-incubator/pymedx/issues. + +If you are reporting a bug, please include: + +- Your operating system name and version. +- Any details about your local setup that might be helpful in troubleshooting. +- Detailed steps to reproduce the bug. + +### Fix Bugs + +Look through the GitHub issues for bugs. Anything tagged with “bug” and “help +wanted” is open to whoever wants to implement it. + +### Implement Features + +Look through the GitHub issues for features. Anything tagged with “enhancement” +and “help wanted” is open to whoever wants to implement it. + +### Write Documentation + +PyMedX could always use more documentation, whether as part of the official +PyMedX docs, in docstrings, or even on the web in blog posts, articles, and +such. + +### Submit Feedback + +The best way to send feedback is to file an issue at +https://github.com/osl-incubator/pymedx/issues. + +If you are proposing a feature: + +- Explain in detail how it would work. +- Keep the scope as narrow as possible, to make it easier to implement. +- Remember that this is a volunteer-driven project, and that contributions are + welcome :) + +## Get Started! + +Ready to contribute? Here’s how to set up `pymedx` for local development. + +1. Fork the `pymedx` repo on GitHub. + +2. Clone your fork locally: + +```bash +$ git clone git@github.com:your_name_here/pymedx.git +``` + +3. Install your local into a conda environment. Assuming you have conda + installed, this is how you set up your fork for local development: + +```bash +$ cd pymedx/ +$ conda env create --file conda/dev.yaml +$ conda activate pymedx +$ poetry install +``` + +4. Create a branch for local development: + +```bash +$ git checkout -b name-of-your-bugfix-or-feature +``` + + Now you can make your changes locally. + +5. When you’re done making changes, check that your changes pass linter and + tests: + +```bash +$ makim tests.linter +$ makim tests.unit +``` + +6. Commit your changes and push your branch to GitHub: + +```bash +$ git add . +$ git commit -m "Your detailed description of your changes." +$ git push origin name-of-your-bugfix-or-feature +``` + +7. Submit a pull request through the GitHub website. + +## Pull Request Guidelines + +Before you submit a pull request, check that it meets these guidelines: + +1. The pull request should include tests. +2. If the pull request adds functionality, the docs should be updated. Put your + new functionality into a function with a docstring, and add the feature to + the list in README.rst. +3. The pull request should work for Python >= 3.8.1 + +## Release + +This project uses semantic-release in order to cut a new release based on the +commit-message. + +### Commit message format + +**semantic-release** uses the commit messages to determine the consumer impact +of changes in the codebase. Following formalized conventions for commit +messages, **semantic-release** automatically determines the next +[semantic version](https://semver.org) number, generates a changelog and +publishes the release. + +By default, **semantic-release** uses +[Angular Commit Message Conventions](https://github.com/angular/angular/blob/master/CONTRIBUTING.md#-commit-message-format). +The commit message format can be changed with the `preset` or `config` options\_ +of the +[@semantic-release/commit-analyzer](https://github.com/semantic-release/commit-analyzer#options) +and +[@semantic-release/release-notes-generator](https://github.com/semantic-release/release-notes-generator#options) +plugins. + +Tools such as [commitizen](https://github.com/commitizen/cz-cli) or +[commitlint](https://github.com/conventional-changelog/commitlint) can be used +to help contributors and enforce valid commit messages. + +The table below shows which commit message gets you which release type when +`semantic-release` runs (using the default configuration): + +| Commit message | Release type | +| -------------------------------------------------------------- | ---------------- | +| `fix(pencil): stop graphite breaking when pressure is applied` | Fix Release | +| `feat(pencil): add 'graphiteWidth' option` | Feature Release | +| `perf(pencil): remove graphiteWidth option` | Chore | +| `BREAKING CHANGE: The graphiteWidth option has been removed` | Breaking Release | + +source: + + +As this project uses the `squash and merge` strategy, ensure to apply the commit +message format to the PR's title. diff --git a/docs/images/favicon.ico b/docs/images/favicon.ico new file mode 100644 index 00000000..c2648358 Binary files /dev/null and b/docs/images/favicon.ico differ diff --git a/docs/images/logo.png b/docs/images/logo.png new file mode 100644 index 00000000..e80a40eb Binary files /dev/null and b/docs/images/logo.png differ diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 00000000..70e3dcfa --- /dev/null +++ b/docs/index.md @@ -0,0 +1,34 @@ +> PyMedX is a fork from a archived project called PyMed: https://github.com/gijswobben/pymedx + +# PyMedX - PubMed Access through Python +PyMedX is a Python library that provides access to PubMed through the PubMed API. + +## Why this library? +The PubMed API is not very well documented and querying it in a performant way is too complicated and time consuming for researchers. This wrapper provides access to the API in a consistent, readable and performant way. + +## Features +This library takes care of the following for you: + +- Querying the PubMed database (with the standard PubMed query language) +- Batching of requests for better performance +- Parsing and cleaning of the retrieved articles + +## Examples +For full (working) examples have a look at the `examples/` folder in this repository. In essence you only need to import the `PubMed` class, instantiate it, and use it to query: + +```python +from pymedx import PubMed +pubmed = PubMed(tool="MyTool", email="my@email.address") +results = pubmed.query("Some query", max_results=500) +``` + +## Notes on the API +The original documentation of the PubMed API can be found here: [PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/tools/developers/). PubMed Central kindly requests you to: + +> - Do not make concurrent requests, even at off-peak times; and +> - Include two parameters that help to identify your service or application to our servers +> * _tool_ should be the name of the application, as a string value with no internal spaces, and +> * _email_ should be the e-mail address of the maintainer of the tool, and should be a valid e-mail address. + +## Notice of Non-Affiliation and Disclaimer +The author of this library is not affiliated, associated, authorized, endorsed by, or in any way officially connected with PubMed, or any of its subsidiaries or its affiliates. The official PubMed website can be found at https://www.ncbi.nlm.nih.gov/pubmed/. diff --git a/docs/installation.md b/docs/installation.md new file mode 100644 index 00000000..80982676 --- /dev/null +++ b/docs/installation.md @@ -0,0 +1,39 @@ +# Installation + +## Stable release + +To install PyMedX, run this command in your terminal: + +```bash +$ pip install pymedx +``` + +This is the preferred method to install PyMedX, as it will always install the +most recent stable release. + +If you don't have [pip](https://pip.pypa.io) installed, this +[Python installation guide](http://docs.python-guide.org/en/latest/starting/installation/) +can guide you through the process. + +## From sources + +The sources for PyMedX can be downloaded from the +[Github repo](https://github.com/osl-incubator/pymedx). + +You can either clone the public repository: + +```bash +$ git clone https://github.com/osl-incubator/pymedx +``` + +Or download the [tarball](https://github.com/osl-incubator/pymedx/tarball/main): + +```bash +$ curl -OJL https://github.com/osl-incubator/pymedx/tarball/main +``` + +Once you have a copy of the source, you can install it with: + +```bash +$ poetry install +``` diff --git a/examples/advanced_search/main.py b/examples/advanced_search/main.py index 276a6014..3dff429b 100644 --- a/examples/advanced_search/main.py +++ b/examples/advanced_search/main.py @@ -1,4 +1,4 @@ -from pymed import PubMed +from pymedx import PubMed # Create a PubMed object that GraphQL can use to query # Note that the parameters are not required but kindly requested by PubMed Central diff --git a/examples/author_cooccurence_analysis/main.py b/examples/author_cooccurence_analysis/main.py index 5dd9800c..ebc7184d 100644 --- a/examples/author_cooccurence_analysis/main.py +++ b/examples/author_cooccurence_analysis/main.py @@ -1,7 +1,7 @@ import csv import itertools -from pymed import PubMed +from pymedx import PubMed # Create a PubMed object that GraphQL can use to query diff --git a/examples/simple_search/main.py b/examples/simple_search/main.py index 8e0c36f1..88277c10 100644 --- a/examples/simple_search/main.py +++ b/examples/simple_search/main.py @@ -1,4 +1,4 @@ -from pymed import PubMed +from pymedx import PubMed # Create a PubMed object that GraphQL can use to query diff --git a/mkdocs.yaml b/mkdocs.yaml new file mode 100644 index 00000000..3d2ace57 --- /dev/null +++ b/mkdocs.yaml @@ -0,0 +1,149 @@ +site_name: PyMedX +site_url: https://osl-incubator.github.io/pymedx +repo_url: https://github.com/osl-incubator/pymedx +docs_dir: ./docs +site_dir: ./build +# extra_css: +# - stylesheets/extra.css +# Page tree +nav: + - index.md + - Installation: installation.md + - Changelog: changelog.md + - Contributing: contributing.md + - API: api/references.md +theme: + name: material + features: + - content.code.annotate + - content.tabs.link + - header.autohide + - navigation.indexes + - navigation.instant + - search.highlight + - search.share + - search.suggest + icon: + repo: fontawesome/brands/github + logo: images/logo.png + favicon: images/favicon.png + palette: + scheme: slate + primary: white + accent: lime + # custom_dir: docs/overrides +plugins: + - search + - macros + # - autorefs + # - exclude: + # glob: + # - backends/template.md + - mkdocstrings: + enable_inventory: true + handlers: + python: + paths: [../src] + + import: + - https://docs.python.org/3/objects.inv + options: + docstring_style: numpy + filters: + - "!^Bounds" + - "!^__class__" + - "!^_filter_with_like" + - "!^_find_backends" + - "!^_key$" + - "!^_literal_value_hash_key" + - "!^_log" + - "!^_nbytes" + - 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">3.8.1,<4" +requests = ">=2.20.0" + +[tool.poetry.group.dev.dependencies] +pytest = ">=7.3.2" +pytest-cov = ">=4.1.0" +coverage = ">=7.2.7" +pre-commit = ">=3.3.2" +ruff = ">=0.1.5" +mypy = ">=1.6.0" +bandit = ">=1.7.5" +vulture = ">=2.9.1" +mccabe = ">=0.6.1" +ipykernel = ">=6.0.0" +ipython = ">=7.0.0" +mkdocs = ">=1.4.3" +mkdocs-exclude = ">=1.0.2" +mkdocs-jupyter = ">=0.24.1" +mkdocs-literate-nav = ">=0.6.0" +mkdocs-macros-plugin = ">=0.7.0,<1" +mkdocs-material = ">=9.1.15" +mkdocstrings = ">=0.21.2" +mkdocstrings-python = ">=1.1.2" +jupyterlab = ">=4.0.5" +makim = "1.12.0" + +[tool.pytest.ini_options] +testpaths = [ + "tests", +] + +[tool.vulture] +exclude = ["tests"] +ignore_decorators = [] +ignore_names = [] +make_whitelist = true +min_confidence = 80 +paths = ["src/pymedx"] +sort_by_size = true +verbose = false + +[tool.ruff] +line-length = 79 +force-exclude = true +src = ["./"] +ignore = ["PLR0913"] +exclude = [ + 'docs', +] +select = [ + "E", # pycodestyle + "F", # pyflakes + "D", # pydocstyle + "YTT", # flake8-2020 + "PL", # PL + "RUF", # Ruff-specific rules + "I001", # isort +] +fix = true + +[tool.ruff.pydocstyle] +convention = "numpy" + +[tool.ruff.isort] +# Use a single line between direct and from import +lines-between-types = 1 + +[tool.ruff.format] +quote-style = "double" + + +[tool.mypy] +no_strict_optional = false diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 4a0e53ea..00000000 --- a/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -requests>=2.20.0 -gitpython>=2.1.11 -twine>=1.12.1 diff --git a/setup.py b/setup.py deleted file mode 100644 index b78a056c..00000000 --- a/setup.py +++ /dev/null @@ -1,32 +0,0 @@ -import os -from setuptools import setup -from setuptools import find_packages -from pymed.version import __version__ - - -def read(fname): - return open(os.path.join(os.path.dirname(__file__), fname)).read() - - -setup( - name="pymed", - version=__version__, - author="Gijs Wobben", - author_email="gijswobben@gmail.com", - description=("Python library for access to PubMed"), - license="MIT", - keywords="PubMed PMC", - url="https://github.com/gijswobben/pymed", - packages=find_packages(), - install_requires=["requests>=2.20.0"], - tests_require=["pytest"], - long_description_content_type="text/markdown", - long_description=read("README.md"), - classifiers=[ - "Topic :: Utilities", - "Development Status :: 3 - Alpha", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: MIT License", - "Programming Language :: Python :: 3 :: Only", - ], -) diff --git a/src/pymedx/__init__.py b/src/pymedx/__init__.py new file mode 100644 index 00000000..653f8b81 --- /dev/null +++ b/src/pymedx/__init__.py @@ -0,0 +1,21 @@ +# mypy: disable-error-code="attr-defined" +"""PyMedX package.""" +from importlib import metadata as importlib_metadata + +from .api import PubMed + + +def get_version(): + """Return the program version.""" + try: + return importlib_metadata.version(__name__) + except importlib_metadata.PackageNotFoundError: # pragma: no cover + return "0.1.0" # semantic-release + + +version = get_version() + +__version__ = version + + +__all__ = ["PubMed", "__version__"] diff --git a/pymed/api.py b/src/pymedx/api.py similarity index 100% rename from pymed/api.py rename to src/pymedx/api.py diff --git a/pymed/article.py b/src/pymedx/article.py similarity index 100% rename from pymed/article.py rename to src/pymedx/article.py diff --git a/pymed/book.py b/src/pymedx/book.py similarity index 100% rename from pymed/book.py rename to src/pymedx/book.py diff --git a/pymed/helpers.py b/src/pymedx/helpers.py similarity index 100% rename from pymed/helpers.py rename to src/pymedx/helpers.py