diff --git a/.codecov.yml b/.codecov.yml new file mode 100644 index 0000000..090fc45 --- /dev/null +++ b/.codecov.yml @@ -0,0 +1,12 @@ +coverage: + ignore: + - "examples/.*" + - "src/spectrumkit/_version.py" + - "tests/.*" + status: + project: + default: + target: auto + patch: false + +comment: false diff --git a/.github/ISSUE_TEMPLATE/1-bug_report.yml b/.github/ISSUE_TEMPLATE/1-bug_report.yml new file mode 100644 index 0000000..aaa95a6 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/1-bug_report.yml @@ -0,0 +1,78 @@ +name: 🐛 Bug report +description: Create a bug report to help us eliminate issues and improve. +title: "BUG: " +labels: [bug] +body: + - type: markdown + attributes: + value: | + Thanks for taking the time to fill out this bug report! + - type: textarea + id: summary + attributes: + label: Summary + description: A clear and concise description of what the bug is. + placeholder: Describe the bug clearly and concisely. + validations: + required: true + - type: textarea + id: expected_behavior + attributes: + label: Expected behavior + description: | + A clear and concise description of what you want to do and what you think should happen. + (Code and files to reproduce the behavior can be added below). + placeholder: Describe what you expected to happen. + validations: + required: true + - type: textarea + id: actual_behavior + attributes: + label: Actual behavior + description: | + Describe the actual behavior, how it differs from the expected behavior, and how this can be observed. + + Try to be specific and do **not** use vague terms like "doesn't work" or "wrong result". + + Do not assume that the person reading this has any experience with or knowledge of your specific area of research. + placeholder: Describe the actual behavior. + validations: + required: true + - type: input + id: version + attributes: + label: Version + description: | + What versions of spectrumkit and MAICoS are you using and on what platform? You can find them by running: + + ```bash + python -c "import spectrumkit, maicos; print(spectrumkit.__version__, maicos.__version__)" + python -V + ``` + placeholder: e.g., 0.1.0, 0.13 + validations: + required: true + - type: textarea + id: steps_to_reproduce + attributes: + label: Steps to reproduce + description: | + Describe the steps required to (quickly) reproduce the issue. + + You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. + + Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. + + **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes that somebody will look into it and fix the problem. + placeholder: List the steps to reproduce here. + validations: + required: false + - type: textarea + id: further_info + attributes: + label: Further information, files, and links + description: | + Any relevant information that might help us to understand the issue. + placeholder: Add relevant files, logs, or links here. + validations: + required: false diff --git a/.github/ISSUE_TEMPLATE/2-documentation_issue.yml b/.github/ISSUE_TEMPLATE/2-documentation_issue.yml new file mode 100644 index 0000000..9a5f8f4 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/2-documentation_issue.yml @@ -0,0 +1,45 @@ +name: 📚 Documentation issue +description: Report an issue related to the documentation. +title: "DOC: " +labels: [documentation] +body: + - type: markdown + attributes: + value: | + Report a mistake, missing information, or improvement suggestion related to the documentation. + - type: textarea + id: location + attributes: + label: Location of the issue + description: | + Provide the location of the documentation issue. This could be a URL, file path, or section heading. + placeholder: e.g., https://maicos-devel.github.io/spectrumkit/stable/get-started/installation.html or "Getting started -> Installation" + validations: + required: true + - type: textarea + id: description + attributes: + label: Description of the issue + description: | + Describe the issue you found. Be as specific as possible. + For example: typo, outdated information, unclear explanation, missing example, etc. + placeholder: Describe the problem clearly. + validations: + required: true + - type: textarea + id: suggestion + attributes: + label: Suggested fix or improvement (optional) + description: | + If you have an idea of how to fix or improve the documentation, please share it here. + placeholder: Suggest the corrected text or improvement. + validations: + required: false + - type: textarea + id: additional_context + attributes: + label: Additional context + description: Add any other context, screenshots, or links that might help clarify the issue. + placeholder: Additional context, links, or screenshots. + validations: + required: false diff --git a/.github/ISSUE_TEMPLATE/3-feature_request.yml b/.github/ISSUE_TEMPLATE/3-feature_request.yml new file mode 100644 index 0000000..ed062a1 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/3-feature_request.yml @@ -0,0 +1,43 @@ +name: ✨ Feature request +description: Suggest an idea or improvement. +title: "FEATURE: " +labels: [enhancement] +body: + - type: markdown + attributes: + value: | + Suggest an idea or improvement for this project. + - type: textarea + id: problem_description + attributes: + label: Is your feature request related to a problem? Please describe. + description: | + A clear and concise description of what the problem is. + Example: "I'm always frustrated when [...]" + placeholder: Describe the problem you are facing or the motivation for the feature. + validations: + required: true + - type: textarea + id: solution + attributes: + label: Describe the solution you'd like + description: A clear and concise description of what you want to happen. + placeholder: Describe the ideal solution or feature you would like to see. + validations: + required: true + - type: textarea + id: alternatives + attributes: + label: Describe alternatives you've considered + description: A clear and concise description of any alternative solutions or features you've considered. + placeholder: Mention any workarounds or alternative ideas you have explored. + validations: + required: false + - type: textarea + id: additional_context + attributes: + label: Additional context + description: Add any other context or screenshots about the feature request here. + placeholder: Provide links, images, or related discussions if available. + validations: + required: false diff --git a/.github/ISSUE_TEMPLATE/4-blank_issue.yml b/.github/ISSUE_TEMPLATE/4-blank_issue.yml new file mode 100644 index 0000000..2e074f0 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/4-blank_issue.yml @@ -0,0 +1,12 @@ +name: 📝 Blank issue +description: Create a new issue from scratch. +body: + - type: textarea + id: description + attributes: + label: Description of the issue + description: | + Describe the issue you found. Be as specific as possible. + placeholder: Describe the problem clearly. + validations: + required: true diff --git a/.github/ISSUE_TEMPLATE/Bug.md b/.github/ISSUE_TEMPLATE/Bug.md deleted file mode 100644 index de38271..0000000 --- a/.github/ISSUE_TEMPLATE/Bug.md +++ /dev/null @@ -1,45 +0,0 @@ ---- -name: Bug report -about: Create a report to help us improve - ---- - -**Expected behavior** - - - -**Actual behavior** - - - - -**Code to reproduce the behavior** - - - -**Current version** - - - -**Describe the solution you'd like** - - -**Describe alternatives you've considered** - - -**Additional context** - diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 0000000..2e1eece --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,5 @@ +blank_issues_enabled: false +contact_links: + - name: 💬 Questions & Discussions + url: https://discord.gg/mnrEQWVAed + about: Please ask and answer questions on our discord server. diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 7a3d9c3..bdcb0d0 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -31,15 +31,17 @@ jobs: check-latest: true - name: Install dependencies - run: python -m pip install wheel build tox + run: python -m pip install tox - - name: Test build integrity + - name: Test build integrity and build sdist run: tox -e build - uses: actions/upload-artifact@v7 with: - name: build - path: dist/* + name: files + path: | + dist/*.tar.gz + dist/*.whl release: name: Release package diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 52815d0..6d77496 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -24,11 +24,15 @@ jobs: check-latest: true - name: install dependencies - run: python -m pip install tox + run: python -m pip install tox gitpython - name: build documentation run: tox -e docs + - name: Check for Changelog + if: github.event_name == 'pull_request' + run: python ./developer/check_changelog.py + - name: put documentation in the website run: | git clone https://github.com/$GITHUB_REPOSITORY --branch gh-pages gh-pages diff --git a/.github/workflows/tests-dev.yml b/.github/workflows/tests-dev.yml new file mode 100644 index 0000000..9ec020a --- /dev/null +++ b/.github/workflows/tests-dev.yml @@ -0,0 +1,58 @@ +name: Tests dev + +on: + schedule: + # check once a week on mondays + - cron: '0 10 * * 1' + +jobs: + tests-dev: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.11", "3.14"] + + steps: + - uses: actions/checkout@v7 + with: + fetch-depth: 0 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v7 + with: + python-version: ${{ matrix.python-version }} + + - name: Install tests dependencies + run: python -m pip install tox + + - name: Run tests against MAICoS dev version + run: tox -e tests-dev + + tests-release: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.11", "3.14"] + + steps: + - uses: actions/checkout@v7 + with: + fetch-depth: 0 + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v7 + with: + python-version: ${{ matrix.python-version }} + + # v0.1.0 predates tests/requirements.txt, so install them before the checkout + - name: Install released spectrumkit and test dependencies + run: | + python -m pip install spectrumkit + python -m pip install -r tests/requirements.txt + python -m pip list + + - name: Check out latest release tag + run: git checkout $(git describe --tags --abbrev=0) + + - name: Run tests against released versions + run: pytest diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 97ef7f7..00a9265 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -11,13 +11,19 @@ on: jobs: tests: - runs-on: ubuntu-24.04 - name: Python ${{ matrix.python-version }} + runs-on: ${{ matrix.os }} + name: ${{ matrix.os }} / Python ${{ matrix.python-version }} strategy: matrix: - python-version: - - "3.11" - - "3.14" + include: + - os: ubuntu-latest + python-version: "3.11" + - os: ubuntu-latest + python-version: "3.14" + - os: macos-latest + python-version: "3.14" + - os: windows-latest + python-version: "3.14" steps: - uses: actions/checkout@v7 @@ -33,13 +39,13 @@ jobs: - run: python -m pip install tox coverage[toml] - name: run Python tests - run: | - tox -e tests - # coverage xml + run: tox -e tests + - name: generate coverage report + run: coverage xml - # - name: upload to codecov.io - # uses: codecov/codecov-action@v5 - # with: - # fail_ci_if_error: true - # files: tests/coverage.xml - # token: ${{ secrets.CODECOV_TOKEN }} + - name: upload to codecov.io + uses: codecov/codecov-action@v7 + with: + fail_ci_if_error: true + files: coverage.xml + token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.readthedocs.yml b/.readthedocs.yml index 421e1bf..b91d6ff 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -24,3 +24,5 @@ python: - requirements: docs/requirements.txt - method: pip path: . + extra_requirements: + - examples diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 7add0f2..9e72ff2 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -11,6 +11,12 @@ The rules for spectrumkit's CHANGELOG file: .. inclusion-marker-changelog-start +Unreleased +---------- + +- Fix logarithmic binning with ``binafter=0`` (#23). +- Require ``maicos>=0.13``, drop the ``mdacli<=0.1.35`` pin. (#20) + v0.1.0 (2026/05/20) ------------------- diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst new file mode 100644 index 0000000..fb49a2b --- /dev/null +++ b/CONTRIBUTING.rst @@ -0,0 +1,133 @@ +Spectrumkit is a community effort, driven mainly by scientists working on +molecular simulations of fluids. It is developed in open collaboration by the MAICoS +developer team and contributors from across the world. +As such, we welcome contributions from anyone who is interested in improving +Spectrumkit, and we are committed to providing a welcoming and inclusive environment for +all contributors. + +To ensure a positive and productive experience for everyone involved in the project, +we have established the following guidelines for contributing. +Please read them carefully before submitting any contributions to Spectrumkit. + +Code of Conduct +--------------- + +As contributors and maintainers of Spectrumkit, we pledge to respect all people who +contribute through reporting issues, posting feature requests, updating documentation, +submitting merge requests or patches, and other activities. + +We are committed to making participation in this project a harassment-free experience +for everyone, regardless of level of experience, gender, gender identity and expression, +sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or +religion. + +Examples of unacceptable behavior by participants include the use of sexual language or +imagery, derogatory comments or personal attacks, trolling, public or private +harassment, insults, or other unprofessional conduct. + +Project maintainers have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are not +aligned to this Code of Conduct. Project maintainers who do not follow the Code of +Conduct may be removed from the project team. + +This code of Conduct applies both within project spaces and in public spaces when an +individual is representing the project or its community. + +Instances of abusive, harassing, or otherwise unacceptable behavior should be +reported to the `project maintainers`_. + +This Code of Conduct is adapted from the `Contributor Covenant`_, version 1.1.0, +available at https://contributor-covenant.org/version/1/1/0/ + +.. _`project maintainers` : https://github.com/maicos-devel/spectrumkit/blob/main/AUTHORS.rst +.. _`Contributor Covenant` : https://contributor-covenant.org + +Getting involved +---------------- + +Contribution via pull requests are always welcome. Source code is available from +`GitHub`_. Before submitting a pull request, please open an issue to discuss your +changes. Use only the ``main`` branch for submitting your requests. + +.. _`GitHub` : https://github.com/maicos-devel/spectrumkit/ + +By contributing to Spectrumkit, you accept and agree to the following terms and +conditions for your present and future contributions submitted to Spectrumkit. Except for +the license granted herein to Spectrumkit and recipients of software distributed by +Spectrumkit, you reserve all right, title, and interest in and to your contributions. + +Getting started +--------------- + +To help with developing start by installing the development dependencies. Our continuous +integration pipeline is based on Tox_. So you need to install ``tox`` first + +.. code-block:: bash + + pip install tox + # or + conda install -c conda-forge tox + +Then go to the `Spectrumkit develop project`_ page, hit the ``Fork`` button and clone +your forked branch to your machine. + +.. code-block:: bash + + git clone git@github.com:your-user-name/spectrumkit.git + +Now you have a local version on your machine which you can install by + +.. code-block:: bash + + cd spectrumkit + pip install -e . + +This install the package in development mode, making it importable globally and allowing +you to edit the code and directly use the updated version. + +To run the tests, the linters, or build the documentation use + +.. code-block:: bash + + tox -e tests + tox -e lint + tox -e docs + +.. _Tox: https://tox.readthedocs.io/en/latest/ +.. _`Spectrumkit develop project` : https://github.com/maicos-devel/spectrumkit + +Useful developer scripts +------------------------ + +The following scripts can be useful to developers: + +- ``./developer/clean_dist_check.py``: Clean dist files. Useful before/after ``tox -e + build`` +- ``./developer/check_changelog.py``: Check that the CHANGELOG has been updated with + respect to the ``main`` branch. + +Automated Contributions Policy +------------------------------ + +Contributing to Spectrumkit requires human judgment, contextual understanding, and +familiarity with concepts related to spectra from molecular simulations. +It is not suitable for automatic processing by AI tools. + +Please refrain from submitting issues or pull requests generated by +fully-automated tools. Maintainers reserve the right, at their sole discretion, +to close such submissions and to block any account responsible for them. + +Review all code or documentation changes made by AI tools and make sure you +understand all changes and can explain them on request, before submitting them +under your name. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/MANIFEST.in b/MANIFEST.in index 6d40ecf..57fa786 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,25 +1,19 @@ graft src -recursive-include docs *.bib -recursive-include docs *.py -recursive-include docs *.rst -recursive-include docs *.svg -recursive-include docs *.txt -prune docs/build -prune docs/src/generated_examples -include AUTHORS.rst -include CHANGELOG.rst -include README.rst -include MANIFEST.in +include *.rst +include LICENSE prune .tox prune developer +prune docs prune examples prune tests +prune .github exclude .gitattributes exclude .gitignore -exclude tox.ini exclude .readthedocs.yml +exclude .codecov.yml +exclude tox.ini global-exclude *.py[cod] __pycache__/* *.so *.dylib diff --git a/developer/check_changelog.py b/developer/check_changelog.py new file mode 100755 index 0000000..dde67bd --- /dev/null +++ b/developer/check_changelog.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python +"""Check if the CHANGELOG has been modified with respect to the main branch.""" +import os + +import git + + +class ChangelogError(Exception): + """Changelog error.""" + + pass + + +changelog = "CHANGELOG.rst" +repo_path = os.path.realpath(os.path.join(os.path.dirname(__file__), "..")) + +repo = git.Repo(repo_path) + +file = repo.git.show(f"origin/main:{changelog}") + +with open(os.path.join(repo_path, changelog)) as f: + workfile = f.read() + +if file.strip() == workfile.strip(): + # Check for changed files and ignore .github/ changes + head_commit = repo.head.commit + diff = head_commit.diff("origin/main") + changed_files = [] + for x in diff: + if x.a_blob.path not in changed_files: + changed_files.append(x.a_blob.path) + if x.b_blob is not None and x.b_blob.path not in changed_files: + changed_files.append(x.b_blob.path) + changed_files = [x for x in changed_files if not x.startswith(".github/")] + + if len(changed_files) > 0: + raise ChangelogError("You have not updated the CHANGELOG file. Please " + f"add a summary of your additions to {changelog}.") + else: + print("No changes detected.") +else: + print("CHANGELOG is up to date.") diff --git a/docs/src/analysis-modules/dielectricspectrum.rst b/docs/src/analysis-modules/dielectricspectrum.rst old mode 100755 new mode 100644 diff --git a/docs/src/api-documentation/lib/index.rst b/docs/src/api-documentation/lib/index.rst index e5bc7b3..ff55add 100644 --- a/docs/src/api-documentation/lib/index.rst +++ b/docs/src/api-documentation/lib/index.rst @@ -3,7 +3,7 @@ Library functions ################# -.. automodule:: maicos.lib +.. automodule:: spectrumkit.lib .. toctree:: :titlesonly: @@ -11,4 +11,5 @@ Library functions :caption: Library functions math + preprocessing util diff --git a/docs/src/api-documentation/lib/preprocessing.rst b/docs/src/api-documentation/lib/preprocessing.rst new file mode 100644 index 0000000..a9443d7 --- /dev/null +++ b/docs/src/api-documentation/lib/preprocessing.rst @@ -0,0 +1,9 @@ +.. _preprocessing_helper_functions: + +Preprocessing helper functions +############################## + +.. automodule:: spectrumkit.lib.preprocessing + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/conf.py b/docs/src/conf.py index 18bd71b..5a6fcd0 100644 --- a/docs/src/conf.py +++ b/docs/src/conf.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python -# # Copyright (c) 2025 Authors and contributors # (see the AUTHORS.rst file for the full list of names) # @@ -116,9 +114,9 @@ # font-awesome logos html_css_files = [ - "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/fontawesome.min.css", # noqa: E501 - "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/solid.min.css", # noqa: E501 - "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/brands.min.css", # noqa: E501 + "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/fontawesome.min.css", + "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/solid.min.css", + "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.0.0/css/brands.min.css", ] # -- Options for HTMLHelp output --------------------------------------------- @@ -129,7 +127,7 @@ # -- Extension configuration ------------------------------------------------- # Configuration for intersphinx: refer to the Python standard library -# and other packages used by MAICoS +# and other packages used by spectrumkit intersphinx_mapping = { "scipy": ("https://docs.scipy.org/doc/scipy/", None), "matplotlib": ("https://matplotlib.org/stable/", None), diff --git a/docs/src/get-started/changelog.rst b/docs/src/get-started/changelog.rst old mode 100755 new mode 100644 diff --git a/docs/src/get-started/installation.rst b/docs/src/get-started/installation.rst old mode 100755 new mode 100644 diff --git a/docs/src/get-started/units.rst b/docs/src/get-started/units.rst index bd92930..cdbaa96 100644 --- a/docs/src/get-started/units.rst +++ b/docs/src/get-started/units.rst @@ -1,7 +1,7 @@ Some conventions ---------------- -The base units of Scatterkit are consistent with those of `MDAnalysis`_. Keeping inputs and +The base units of Spectrumkit are consistent with those of `MDAnalysis`_. Keeping inputs and outputs consistent with this set of units reduces ambiguity, so we encourage everyone to use them exclusively. diff --git a/docs/src/get-started/usage-python.rst b/docs/src/get-started/usage-python.rst index 88fa041..9d99b51 100644 --- a/docs/src/get-started/usage-python.rst +++ b/docs/src/get-started/usage-python.rst @@ -9,4 +9,4 @@ To use Spectrumkit using the Python interpreter see the Molecular Analysis for Interfacial and Confined Systems toolkit. .. _MAICOS tutorial: - https://maicos-analysis.org/stable/examples/usage-python.html + https://maicos-analysis.org/stable/get-started/basic-usage.html diff --git a/docs/src/index.rst b/docs/src/index.rst index 44ab483..7d740ba 100644 --- a/docs/src/index.rst +++ b/docs/src/index.rst @@ -36,16 +36,16 @@ API Documentation ----------------- The :ref:`userdoc_api-documentation` section is for Spectrumkit for advanced users, it contains technical references and parameter list for the APIs behind the library. It -describes the various functionalities provided by Scatterkit. You can always refer to this -section to learn more about classes, functions, modules, and other aspects of Scatterkit +describes the various functionalities provided by Spectrumkit. You can always refer to this +section to learn more about classes, functions, modules, and other aspects of Spectrumkit machinery you may come across behind the analysis classes described in :ref:`userdoc-analysis-modules`. Concepts & Explanations ----------------------- The :ref:`userdoc-concepts-explanations` section discusses key topics and concepts at a -fairly high level and provides explanations to expand your knowledge of Scatterkit. It -requires at least basic to intermediate knowledge of Scatterkit. +fairly high level and provides explanations to expand your knowledge of Spectrumkit. It +requires at least basic to intermediate knowledge of Spectrumkit. .. toctree:: diff --git a/examples/README.rst b/examples/README.rst index b00184c..625f5ea 100644 --- a/examples/README.rst +++ b/examples/README.rst @@ -6,9 +6,9 @@ How-to guides Like a cooking recipe, How-to guides help you solve key problems and use cases. If you are a total spectrumkit beginner, you should start with the :ref:`userdoc-get-started` section. Otherwise this section consists of introductory examples and examples -demonstrating specific features of scatterkit using its Python API. +demonstrating specific features of spectrumkit using its Python API. -For running the examples install scatterkit with the ``examples`` optional dependencies. +For running the examples install spectrumkit with the ``examples`` optional dependencies. .. code-block:: bash diff --git a/examples/mdanalysis_workflow.py b/examples/mdanalysis_workflow.py index bb1d318..70b1536 100644 --- a/examples/mdanalysis_workflow.py +++ b/examples/mdanalysis_workflow.py @@ -1,4 +1,3 @@ -#!/usr/bin/env python """.. _howto-mdanalysis-workflow: MDAnalysis Workflow @@ -11,6 +10,7 @@ """ import MDAnalysis as mda + from spectrumkit import DielectricSpectrum # %% @@ -49,8 +49,9 @@ print(f"Average volume: {analysis.results.V:.2f} Ų") print(f"Number of frames: {len(analysis.results.P)}") print(f"Frequency points: {len(analysis.results.nu)}") -print(f"Frequency range: {analysis.results.nu[0]:.4f} - " - f"{analysis.results.nu[-1]:.4f} THz") +print( + f"Frequency range: {analysis.results.nu[0]:.4f} - {analysis.results.nu[-1]:.4f} THz" +) # %% # diff --git a/pyproject.toml b/pyproject.toml index 5f9cd14..fcc05da 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -38,7 +38,7 @@ classifiers = [ "Topic :: Scientific/Engineering :: Physics", "Topic :: Software Development :: Libraries :: Python Modules", ] -dependencies = ["maicos>=0.11.2", "mdacli<=0.1.35"] +dependencies = ["maicos>=0.13"] dynamic = ["version"] [project.optional-dependencies] @@ -51,32 +51,56 @@ issues = "https://github.com/maicos-devel/spectrumkit/issues" [tool.check-manifest] # ignore files missing in VCS -ignore = ["src/spectrumkit/_version.py", "docs/src/sg_execution_times.rst"] +ignore = ["src/spectrumkit/_version.py"] [tool.mypy] -exclude = ["docs/src/examples"] +exclude = ["docs/src/generated_examples"] follow_imports = 'skip' ignore_missing_imports = true [tool.coverage.paths] source = ["src/spectrumkit", "*/site-packages"] +[tool.coverage.run] +omit = [ + "examples/*", + "src/spectrumkit/_version.py", + "tests/*", + "tests/**/*", + "*/tests/*", + "*/tests/**/*", +] + [tool.coverage.report] skip_covered = true show_missing = true +exclude_lines = [ + "if __name__ == .__main__.:", + "if TYPE_CHECKING:", + "\\.\\.\\.", +] +omit = [ + "examples/*", + "src/spectrumkit/_version.py", + "tests/*", + "tests/**/*", + "*/tests/*", + "*/tests/**/*", +] [tool.pytest.ini_options] testpaths = "tests" python_files = ["test_*.py", "*_test.py", "tests.py"] +filterwarnings = ["error"] addopts = [ "--cov", "--cov-append", "--cov-report=", "--import-mode=append", - "--disable-warnings", ] [tool.ruff] +exclude = ["docs/src/generated_examples/**", "src/spectrumkit/_version.py"] line-length = 88 [tool.ruff.lint] @@ -117,6 +141,14 @@ ignore = [ "LOG015", # Logging using root logger #TODO(@PicoCentauri): Check this ] +[tool.ruff.lint.per-file-ignores] +"**/{docs,examples}/*" = [ + "T20", # Don't require any docstrings in these directories + "D212", # docstring summary not starting at first line + "D205", # 1 blank line required between summary line and description + "D415", # sphinx-gallery labels precede the summary line +] + [tool.ruff.lint.isort] known-first-party = ["spectrumkit"] diff --git a/src/spectrumkit/dielectricspectrum.py b/src/spectrumkit/dielectricspectrum.py old mode 100755 new mode 100644 index 9731636..f50b98c --- a/src/spectrumkit/dielectricspectrum.py +++ b/src/spectrumkit/dielectricspectrum.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python -# # Copyright (c) 2025 Authors and contributors # (see the AUTHORS.rst file for the full list of names) # @@ -183,12 +181,14 @@ def calculate_spectrum_from_dipole( # Bin data if there are too many points if not nobin and seglen > bins: + # the zero frequency always stays unbinned, the log spacing can't start at 0 + unbinned = max(binafter, 1) bin_indices = np.logspace( - np.log(binafter) / np.log(10), + np.log(unbinned) / np.log(10), np.log(len(susc)) / np.log(10), bins - binafter + 1, ).astype(int) - bin_indices = np.unique(np.append(np.arange(binafter), bin_indices))[:-1] + bin_indices = np.unique(np.append(np.arange(unbinned), bin_indices))[:-1] results["nu_binned"] = bin(nu, bin_indices) results["susc_binned"] = bin(susc, bin_indices) @@ -353,12 +353,14 @@ def calculate_spectrum_from_current( # Bin data if there are too many points if not nobin and seglen > bins: + # the zero frequency always stays unbinned, the log spacing can't start at 0 + unbinned = max(binafter, 1) bin_indices = np.logspace( - np.log(binafter) / np.log(10), + np.log(unbinned) / np.log(10), np.log(len(susc)) / np.log(10), bins - binafter + 1, ).astype(int) - bin_indices = np.unique(np.append(np.arange(binafter), bin_indices))[:-1] + bin_indices = np.unique(np.append(np.arange(unbinned), bin_indices))[:-1] results["nu_binned"] = bin(nu, bin_indices) results["susc_binned"] = bin(susc, bin_indices) diff --git a/src/spectrumkit/lib/__init__.py b/src/spectrumkit/lib/__init__.py new file mode 100644 index 0000000..177bcff --- /dev/null +++ b/src/spectrumkit/lib/__init__.py @@ -0,0 +1,16 @@ +# Copyright (c) 2025 Authors and contributors +# (see the AUTHORS.rst file for the full list of names) +# +# Released under the GNU Public Licence, v3 or any higher version +# SPDX-License-Identifier: GPL-3.0-or-later +"""Library modules of spectrumkit. + +This library contains general and mathematical helper functions, which are used in +the analysis modules. +""" + +__all__ = [ + "math", + "preprocessing", + "util", +] diff --git a/src/spectrumkit/lib/util.py b/src/spectrumkit/lib/util.py index 46786ba..694722d 100644 --- a/src/spectrumkit/lib/util.py +++ b/src/spectrumkit/lib/util.py @@ -28,7 +28,7 @@ def bin(a: np.ndarray, bins: np.ndarray) -> np.ndarray: The "bins" array should contain the INDEX (integer) where each bin begins. """ - if np.iscomplex(a).any(): + if np.iscomplexobj(a): avg = np.zeros(len(bins), dtype=complex) # average of data else: avg = np.zeros(len(bins)) diff --git a/tests/requirements.txt b/tests/requirements.txt new file mode 100644 index 0000000..9955dec --- /dev/null +++ b/tests/requirements.txt @@ -0,0 +1,2 @@ +pytest +pytest-cov diff --git a/tests/tests.py b/tests/tests.py index acaf8dc..4ac43aa 100644 --- a/tests/tests.py +++ b/tests/tests.py @@ -134,6 +134,23 @@ def test_basic_calculation(self): assert results["susc"].dtype == complex assert results["dsusc"].dtype == complex + def test_binning_without_unbinned_points(self): + """Test logarithmic binning when no low-frequency points stay unbinned.""" + rng = np.random.default_rng(0) + results = calculate_spectrum_from_dipole( + dipole_moment=rng.standard_normal((1000, 3)), + dt=1.0, + volume=1000.0, + temperature=300.0, + segs=1, + bins=5, + binafter=0, + ) + + # the zero frequency stays on its own, the rest is binned logarithmically + assert results["nu_binned"][0] == results["nu"][0] + assert 1 < len(results["nu_binned"]) <= 6 + def test_consistency_with_dielectric_spectrum(self, monkeypatch, tmp_path): """Test that standalone function gives same results as class method.""" monkeypatch.chdir(tmp_path) diff --git a/tox.ini b/tox.ini index 0f73e6a..262409e 100644 --- a/tox.ini +++ b/tox.ini @@ -7,19 +7,18 @@ envlist = lint build tests + docs lint_folders = "{toxinidir}/src" \ - "{toxinidir}/tests" + "{toxinidir}/tests" \ + "{toxinidir}/examples" \ + "{toxinidir}/docs/src/" # configures which environments run with each python version [testenv] # Passing through all enviroment variables to tox jobs passenv = * -platform = - linux: linux - macos: darwin - windows: win32 # Default package_env, used for building source distribution [testenv:.pkg] @@ -28,19 +27,21 @@ platform = [testenv:tests] description = Run test suite with pytest and {basepython}. usedevelop = true -deps = - coverage[toml] - hypothesis - pytest - pytest-cov - pytest-mock - setuptools +deps = -r tests/requirements.txt commands = # Run unit tests pytest {posargs} - # Run documentation tests on all Python files and the README.rst - ; pytest --doctest-modules --pyargs spectrumkit + # Run documentation tests on all Python files + pytest --doctest-modules --pyargs spectrumkit + +[testenv:tests-dev] +description = Run test suite against MAICoS dev version +deps = + -r tests/requirements.txt + maicos @ git+https://github.com/maicos-devel/maicos.git +commands = + pytest {posargs} [testenv:lint] description = Run linters and type checks @@ -56,14 +57,20 @@ commands = sphinx-lint \ --enable all \ --disable line-too-long \ - -i "{toxinidir}/docs/src/examples" \ - {[tox]lint_folders} "{toxinidir}/README.rst" + -i "{toxinidir}/docs/src/generated_examples" \ + {[tox]lint_folders} \ + "{toxinidir}/README.rst" \ + "{toxinidir}/AUTHORS.rst" \ + "{toxinidir}/CHANGELOG.rst" \ + "{toxinidir}/CONTRIBUTING.rst" + # Enforce the 79 chars/line rule stated in the CHANGELOG header + sphinx-lint \ + --disable all \ + --enable line-too-long \ + --max-line-length 79 \ + "{toxinidir}/CHANGELOG.rst" [testenv:build] -platform = - linux: linux - macos: darwin - windows: win32 description = Asserts package build integrity for {platform} with {basepython}. usedevelop = true deps = @@ -71,9 +78,7 @@ deps = check-manifest twine allowlist_externals = - linux: bash - macos: zsh - windows: foreach + bash commands_pre = python {toxinidir}/developer/clean_dist_check.py commands = @@ -81,12 +86,8 @@ commands = twine check dist/*.tar.gz dist/*.whl check-manifest {toxinidir} # Workaround using shells since tox does not support wildcards - linux: bash -c "python -m pip install --force-reinstall dist/spectrumkit-*.tar.gz" - linux: bash -c "python -m pip install --force-reinstall dist/spectrumkit-*.whl" - macos: zsh -c "python -m pip install --force-reinstall dist/spectrumkit-*.tar.gz" - macos: zsh -c "python -m pip install --force-reinstall dist/spectrumkit-*.whl" - windows: foreach ($i in ls dist\*.tar.gz) \{pip install --force-reinstall $i\} - windows: foreach ($i in ls dist\*.whl) \{pip install --force-reinstall $i\} + bash -c "python -m pip install --force-reinstall dist/spectrumkit-*.tar.gz" + bash -c "python -m pip install --force-reinstall dist/spectrumkit-*.whl" [testenv:docs] description = Building the package documentation.