diff --git a/.codecov.yml b/.codecov.yml new file mode 100644 index 0000000..4af5eb2 --- /dev/null +++ b/.codecov.yml @@ -0,0 +1,14 @@ +coverage: + status: + project: # more options at https://docs.codecov.com/docs/commit-status + default: + target: auto # use the coverage from the base commit, fail if coverage is lower + threshold: 0% # allow the coverage to drop by + +comment: + layout: " diff, flags, files" + behavior: default + require_changes: false + require_base: false # [true :: must have a base report to post] + require_head: false # [true :: must have a head report to post] + hide_project_coverage: false # [true :: only show coverage on the git diff aka patch coverage] diff --git a/.codespell/ignore_lines.txt b/.codespell/ignore_lines.txt new file mode 100644 index 0000000..07fa7c8 --- /dev/null +++ b/.codespell/ignore_lines.txt @@ -0,0 +1,2 @@ +;; Please include filenames and explanations for each ignored line. +;; See https://docs.openverse.org/meta/codespell.html for docs. diff --git a/.codespell/ignore_words.txt b/.codespell/ignore_words.txt new file mode 100644 index 0000000..04b4fcf --- /dev/null +++ b/.codespell/ignore_words.txt @@ -0,0 +1,8 @@ +;; Please include explanations for each ignored word (lowercase). +;; See https://docs.openverse.org/meta/codespell.html for docs. + +;; abbreviation for "materials" often used in a journal title +mater + +;; Frobenius norm used in np.linalg.norm +fro diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..88077af --- /dev/null +++ b/.flake8 @@ -0,0 +1,13 @@ +# As of now, flake8 does not natively support configuration via pyproject.toml +# https://github.com/microsoft/vscode-flake8/issues/135 +[flake8] +exclude = + .git, + __pycache__, + build, + dist, + docs/source/conf.py +max-line-length = 79 +# Ignore some style 'errors' produced while formatting by 'black' +# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings +extend-ignore = E203 diff --git a/.github/ISSUE_TEMPLATE/bug_feature.md b/.github/ISSUE_TEMPLATE/bug_feature.md new file mode 100644 index 0000000..b3454de --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_feature.md @@ -0,0 +1,16 @@ +--- +name: Bug Report or Feature Request +about: Report a bug or suggest a new feature! +title: "" +labels: "" +assignees: "" +--- + +### Problem + + + +### Proposed solution diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md new file mode 100644 index 0000000..56bcd01 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/release_checklist.md @@ -0,0 +1,46 @@ +--- +name: Release +about: Checklist and communication channel for PyPI and GitHub release +title: "Ready for PyPI/GitHub release" +labels: "release" +assignees: "" +--- + +### PyPI/GitHub rc-release preparation checklist: + +- [ ] All PRs/issues attached to the release are merged. +- [ ] All the badges on the README are passing. +- [ ] License information is verified as correct. If you are unsure, please comment below. +- [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are + missing), tutorials, and other human-written text is up-to-date with any changes in the code. +- [ ] Installation instructions in the README, documentation, and the website are updated. +- [ ] Successfully run any tutorial examples or do functional testing with the latest Python version. +- [ ] Grammar and writing quality are checked (no typos). +- [ ] Install `pip install build twine`, run `python -m build` and `twine check dist/*` to ensure that the package can be built and is correctly formatted for PyPI release. + +Please tag the maintainer (e.g., @username) in the comment here when you are ready for the PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here: + +### PyPI/GitHub full-release preparation checklist: + +- [ ] Create a new conda environment and install the rc from PyPI (`pip install ==??`) +- [ ] License information on PyPI is correct. +- [ ] Docs are deployed successfully to `https:///`. +- [ ] Successfully run all tests, tutorial examples or do functional testing. + +Please let the maintainer know that all checks are done and the package is ready for full release. + +### conda-forge release preparation checklist: + + + +- [ ] Ensure that the full release has appeared on PyPI successfully. +- [ ] New package dependencies listed in `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock. +- [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions. +- [ ] Tag the maintainer for conda-forge release. + +### Post-release checklist + + + +- [ ] Run tutorial examples and conduct functional testing using the installation guide in the README. Attach screenshots/results as comments. +- [ ] Documentation (README, tutorials, API references, and websites) is deployed without broken links or missing figures. diff --git a/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md new file mode 100644 index 0000000..1099d86 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md @@ -0,0 +1,15 @@ +### What problem does this PR address? + + + +### What should the reviewer(s) do? + + + + diff --git a/.github/workflows/build-wheel-release.yml b/.github/workflows/build-wheel-release.yml new file mode 100644 index 0000000..14c1dc3 --- /dev/null +++ b/.github/workflows/build-wheel-release.yml @@ -0,0 +1,230 @@ +name: Build Wheels and Release + +on: + workflow_dispatch: + push: + tags: + - "*" + +env: + PYTHON_VERSIONS: '["3.11","3.12","3.13"]' + +permissions: + contents: write + actions: read + packages: write + +concurrency: + group: build-wheels-${{ github.ref }} + cancel-in-progress: true + +defaults: + run: + shell: bash {0} + +jobs: + get-python-versions: + runs-on: ubuntu-latest + outputs: + py_ver: ${{ steps.set.outputs.py_ver }} + py_last: ${{ steps.set.outputs.py_last }} + steps: + - id: set + run: | + echo py_ver=$PYTHON_VERSIONS >> $GITHUB_OUTPUT + echo "py_last=${{ fromJson(env.PYTHON_VERSIONS)[0] }}" >> $GITHUB_OUTPUT + + check-tag-on-main: + runs-on: ubuntu-latest + steps: + - name: Checkout repository with full history + uses: actions/checkout@v4 + with: + token: ${{ secrets.PAT_TOKEN }} + fetch-depth: 0 + + - name: Verify tag + run: | + git fetch origin main + TAG_COMMIT=$(git rev-parse ${{ github.ref_name }}) + if git merge-base --is-ancestor "$TAG_COMMIT" origin/main; then + echo "Tag ${{ github.ref_name }} ($TAG_COMMIT) is contained in main" + else + echo "::error::Tag ${{ github.ref_name }} ($TAG_COMMIT) is not found in main. Please release from the main branch." + exit 1 + fi + + check-tag-privilege: + # No third party actions used + uses: scikit-package/release-scripts/.github/workflows/_check-tag-privilege.yml@v0 + with: + maintainer_github_username: sbillinge + + build-sdist: + needs: [check-tag-privilege, get-python-versions, check-tag-on-main] + runs-on: ubuntu-latest + + steps: + - name: Checkout + # GitHub officially-maintained actions + uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Set up Python + # GitHub officially-maintained actions + uses: actions/setup-python@v5 + with: + python-version: ${{ needs.get-python-versions.outputs.py_last }} + + - name: Build docs and remove fonts that blow up the wheel size + run: | + python -m pip install Sphinx sphinx-rtd-theme sphinx-copybutton m2r + cd docs + make html + cd build/html/_static/css/fonts + find . -type f ! -name '*.ttf' -delete + cd ../.. + rm -rf fonts + cd .. + rm -rf _sources + cd .. + rm -rf doctrees + cd ../.. + + - name: Make sdist + run: | + python -m pip install --upgrade pip build cython setuptools setuptools-git-versioning + python -m build --sdist --no-isolation + + - name: Strip source codes + run: | + set -euo pipefail + tar xf dist/diffpy_distanceprinter-*.tar.gz + SRC_DIR=$(find . -maxdepth 1 -type d -name 'diffpy_distanceprinter-*' | head -n1) + find "$SRC_DIR" -type f -name '*.c' -print0 \ + | xargs -0 perl -i.bak -0777 -pe 's{/\*.*?\*/}{}gs' + find "$SRC_DIR" -type f -name '*.c.bak' -delete + tar czf dist/"${SRC_DIR#./}".tar.gz "$SRC_DIR" + rm -rf "$SRC_DIR" + + - name: Upload sdist + # GitHub officially-maintained actions + uses: actions/upload-artifact@v4 + with: + name: sdist + path: dist/ + retention-days: 1 + + - name: Upload INSTRUCTIONS.txt + uses: actions/upload-artifact@v4 + with: + name: instructions + path: INSTRUCTIONS.txt + + build-wheels: + needs: [build-sdist, get-python-versions] + + name: Build wheels ${{ matrix.python }}-${{ matrix.buildplat }} + runs-on: ${{ matrix.buildplat }} + strategy: + fail-fast: false + matrix: + buildplat: + - ubuntu-latest + - macos-14 + - windows-latest + python: ${{ fromJSON(needs.get-python-versions.outputs.py_ver) }} + steps: + - name: Download sdist + # GitHub officially-maintained actions + uses: actions/download-artifact@v4 + with: + name: sdist + path: dist/ + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python }} + + - name: Build wheels + run: | + # setuptools-git-versioning only look into .git and PKG-INFO in the top directory + which python; python --version + which pip; pip --version + python -m pip install --upgrade pip build cython setuptools setuptools-git-versioning + tar xf dist/diffpy_distanceprinter-*.tar.gz + cd diffpy_distanceprinter-* + python -m pip wheel . --no-deps --no-build-isolation --wheel-dir ./../dist + + - name: Upload wheels + uses: actions/upload-artifact@v4 + with: + name: wheels-${{ matrix.python }}-${{ matrix.buildplat }} + path: dist/*.whl + + test-wheels: + needs: [build-wheels, get-python-versions] + + name: Test wheels ${{ matrix.python }}-${{ matrix.buildplat }} + runs-on: ${{ matrix.buildplat }} + strategy: + fail-fast: false + matrix: + buildplat: + - ubuntu-latest + - macos-14 + - windows-latest + python: ${{ fromJson(needs.get-python-versions.outputs.py_ver) }} + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Download wheels + uses: actions/download-artifact@v4 + with: + name: wheels-${{ matrix.python }}-${{ matrix.buildplat }} + path: dist/ + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python }} + + - name: Install wheels + run: | + python -m pip install --upgrade pip pytest setuptools-git-versioning + python -m pip install dist/*.whl + + - name: Assert no source files in installed package + run: | + # For debugging + # touch $(python -c "import sysconfig, os; print(os.path.join(sysconfig.get_paths()['purelib'], 'diffpy/distanceprinter', 'fake.py'))") + python - << 'EOF' + import os, glob, sys, sysconfig + sp = sysconfig.get_paths()['purelib'] + pkg = os.path.join(sp, 'diffpy', 'distanceprinter') + patterns = [os.path.join(pkg, '*.py'), + os.path.join(pkg, '*.c')] + bad = [] + for p in patterns: + bad.extend(glob.glob(p)) + + if bad: + print("Found leftover source files in installed package:") + for f in bad: + print(" -", f) + sys.exit(1) + + print("No .py or .c files present in diffpy/distanceprinter/") + EOF + + - name: Run tests + run: python -m pytest + + release: + needs: [test-wheels] + uses: ./.github/workflows/release-github.yml + secrets: + PAT_TOKEN: ${{ secrets.PAT_TOKEN }} diff --git a/.github/workflows/check-news-item.yml b/.github/workflows/check-news-item.yml new file mode 100644 index 0000000..31a88bf --- /dev/null +++ b/.github/workflows/check-news-item.yml @@ -0,0 +1,12 @@ +name: Check for News + +on: + pull_request_target: + branches: + - main + +jobs: + check-news-item: + uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0 + with: + project: diffpy.distanceprinter diff --git a/.github/workflows/matrix-no-codecov-on-merge-to-main.yml b/.github/workflows/matrix-no-codecov-on-merge-to-main.yml new file mode 100644 index 0000000..48385d1 --- /dev/null +++ b/.github/workflows/matrix-no-codecov-on-merge-to-main.yml @@ -0,0 +1,19 @@ +name: CI + +on: + push: + branches: + - main + release: + types: + - prereleased + - published + workflow_dispatch: + +jobs: + matrix-coverage: + uses: scikit-package/release-scripts/.github/workflows/_matrix-no-codecov-on-merge-to-main.yml@v0 + with: + project: diffpy.distanceprinter + c_extension: false + headless: false diff --git a/.github/workflows/release-github.yml b/.github/workflows/release-github.yml new file mode 100644 index 0000000..be9c891 --- /dev/null +++ b/.github/workflows/release-github.yml @@ -0,0 +1,163 @@ +name: Release on GitHub + +on: + workflow_call: + secrets: + PAT_TOKEN: + description: "GitHub Personal Access Token" + required: true + +env: + TAG: ${{ github.ref_name }} + +defaults: + run: + shell: bash {0} + +jobs: + prepare-release: + if: ${{ ! contains(github.ref, 'rc') }} + runs-on: ubuntu-latest + steps: + - name: Checkout the repository + uses: actions/checkout@v4 + with: + token: ${{ secrets.GITHUB_TOKEN }} + fetch-depth: 0 + ref: main + + - name: Update CHANGELOG + run: | + wget https://raw.githubusercontent.com/scikit-package/release-scripts/v0/.github/workflows/update-changelog.py + python update-changelog.py "$TAG" + rm update-changelog.py + + - name: Commit updated CHANGELOG.rst + run: | + git config user.name "github-actions[bot]" + git config user.email "github-actions[bot]@users.noreply.github.com" + git add . + if ! git diff --cached --quiet; then + git commit -m "update changelog for $TAG" + git push origin main + else + echo "No CHANGELOG.rst changes" + fi + + - name: New tag + run: | + git fetch --tags + git tag -d "$TAG" 2>/dev/null || true + git push origin ":$TAG" 2>/dev/null || true + git tag "$TAG" + git push origin "$TAG" + + - name: Get CHANGELOG.txt + run: | + wget https://raw.githubusercontent.com/scikit-package/release-scripts/v0/.github/workflows/get-latest-changelog.py + python get-latest-changelog.py "$TAG" + rm get-latest-changelog.py + + - name: Upload changelog.txt + uses: actions/upload-artifact@v4 + with: + name: changelog + path: CHANGELOG.txt + + release: + needs: [prepare-release] + if: always() + runs-on: ubuntu-latest + env: + REPO_FULL: ${{ github.repository }} + PAT_TOKEN: ${{ secrets.PAT_TOKEN }} + steps: + - name: Check prepare release + run: | + if [[ ${{ needs.prepare-release.result }} != 'success' && "$TAG" != *rc* ]]; then + echo "::error::Skipping release job because prepare-release failed" + exit 78 + fi + echo "Continuing with release job" + + - name: Download built wheels + uses: actions/download-artifact@v4 + with: + path: dist/ + + - name: Download changelog + if: ${{ needs.prepare-release.result == 'success' }} + uses: actions/download-artifact@v4 + with: + name: changelog + path: . + + - name: Download instructions + uses: actions/download-artifact@v4 + with: + name: instructions + path: . + + - name: Zip wheels and instructions into dist/distanceprinter-$TAG-wheels.zip + run: | + mkdir -p dist + find dist -type f -name '*.whl' | zip -j dist/distanceprinter-"$TAG"-wheels.zip -@ + zip -j dist/distanceprinter-"$TAG"-wheels.zip INSTRUCTIONS.txt + + - name: Prepare release metadata + id: meta + run: | + if [[ "$TAG" == *rc* ]]; then + PRERELEASE=true + TITLE="Pre-release $TAG" + BODY_RAW="Changelog: https://github.com/$REPO_FULL/commits/$TAG" + else + PRERELEASE=false + TITLE="Release $TAG" + BODY_RAW=$( payload.json + + echo "Release metadata:" + cat payload.json + + - name: Create GitHub Release + id: create_release + run: | + set -euo pipefail + + HTTP_STATUS=$( + curl --silent --output resp.json --write-out "%{http_code}" \ + -X POST "https://api.github.com/repos/$REPO_FULL/releases" \ + -H "Accept: application/vnd.github+json" \ + -H "Content-Type: application/json" \ + -H "Authorization: Bearer $PAT_TOKEN" \ + --data @payload.json + ) + if [[ "$HTTP_STATUS" -ne 201 ]]; then + echo "::error::Failed to create release (status $HTTP_STATUS)" + exit 1 + fi + + UPLOAD_URL=$(jq -r .upload_url resp.json | sed 's/{.*}//') + echo "upload_url=$UPLOAD_URL" >> $GITHUB_OUTPUT + + - name: Upload distanceprinter-$TAG-wheels.zip + if: steps.create_release.outputs.upload_url != '' + run: | + FILE=dist/distanceprinter-$TAG-wheels.zip + echo "Uploading asset: $FILE" + curl --silent --fail --data-binary @"$FILE" \ + -H "Content-Type: application/zip" \ + -H "Authorization: Bearer $PAT_TOKEN" \ + "${{ steps.create_release.outputs.upload_url }}?name=$(basename "$FILE")" diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml new file mode 100644 index 0000000..7b4b312 --- /dev/null +++ b/.github/workflows/tests-on-pr.yml @@ -0,0 +1,16 @@ +name: Tests on PR + +on: + pull_request: + workflow_dispatch: + +jobs: + tests-on-pr: + uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr-no-codecov.yml@v0 + with: + project: diffpy.distanceprinter + c_extension: false + headless: false + run: | + conda install pre-commit + pre-commit run --all-files diff --git a/.gitignore b/.gitignore index a122710..099e294 100644 --- a/.gitignore +++ b/.gitignore @@ -1,45 +1,93 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ *.py[cod] +*$py.class # C extensions *.so -# Packages -*.egg -*.egg-info -dist -build -eggs -parts -bin -var -sdist -temp -develop-eggs +# Distribution / packaging +.Python +env/ +build/ +_build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +venv/ +*.egg-info/ .installed.cfg -lib -lib64 -tags +*.egg +bin/ +temp/ +tags/ errors.err +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + # Installer logs pip-log.txt +pip-delete-this-directory.txt MANIFEST # Unit test / coverage reports +htmlcov/ +.tox/ .coverage -.tox +.coverage.* +.cache nosetests.xml +coverage.xml +*,cover +.hypothesis/ # Translations *.mo +*.pot # Mr Developer .mr.developer.cfg .project .pydevproject -.settings -# version information -setup.cfg -/DistancePrinter/version.cfg -/DistancePrinter/gitarchive.cfg +# Django stuff: +*.log + +# Sphinx documentation +docs/build/ +docs/source/generated/ + +# pytest +.pytest_cache/ + +# PyBuilder +target/ + +# Editor files +# mac +.DS_Store +*~ + +# vim +*.swp +*.swo + +# pycharm +.idea/ + +# VSCode +.vscode/ + +# Ipython Notebook +.ipynb_checkpoints diff --git a/.isort.cfg b/.isort.cfg new file mode 100644 index 0000000..86f162b --- /dev/null +++ b/.isort.cfg @@ -0,0 +1,5 @@ +[settings] +# Keep import statement below line_length character limit +line_length = 79 +multi_line_output = 3 +include_trailing_comma = True diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..0e4a84d --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,66 @@ +default_language_version: + python: python3 +ci: + autofix_commit_msg: | + [pre-commit.ci] auto fixes from pre-commit hooks + autofix_prs: true + autoupdate_branch: "pre-commit-autoupdate" + autoupdate_commit_msg: "[pre-commit.ci] pre-commit autoupdate" + autoupdate_schedule: monthly + skip: [no-commit-to-branch] + submodules: false +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: check-yaml + - id: end-of-file-fixer + - id: trailing-whitespace + - id: check-case-conflict + - id: check-merge-conflict + - id: check-toml + - id: check-added-large-files + - repo: https://github.com/psf/black + rev: 24.4.2 + hooks: + - id: black + - repo: https://github.com/pycqa/flake8 + rev: 7.0.0 + hooks: + - id: flake8 + - repo: https://github.com/pycqa/isort + rev: 5.13.2 + hooks: + - id: isort + args: ["--profile", "black"] + - repo: https://github.com/kynan/nbstripout + rev: 0.7.1 + hooks: + - id: nbstripout + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: no-commit-to-branch + name: Prevent Commit to Main Branch + args: ["--branch", "main"] + stages: [pre-commit] + - repo: https://github.com/codespell-project/codespell + rev: v2.3.0 + hooks: + - id: codespell + additional_dependencies: + - tomli + # prettier - multi formatter for .json, .yml, and .md files + - repo: https://github.com/pre-commit/mirrors-prettier + rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8 + hooks: + - id: prettier + additional_dependencies: + - "prettier@^3.2.4" + # docformatter - PEP 257 compliant docstring formatter + - repo: https://github.com/s-weigand/docformatter + rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c + hooks: + - id: docformatter + additional_dependencies: [tomli] + args: [--in-place, --config, ./pyproject.toml] diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 0000000..aaa8889 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,13 @@ +version: 2 + +build: + os: "ubuntu-22.04" + tools: + python: "latest" + +python: + install: + - requirements: requirements/docs.txt + +sphinx: + configuration: docs/source/conf.py diff --git a/AUTHORS.rst b/AUTHORS.rst new file mode 100644 index 0000000..68e8471 --- /dev/null +++ b/AUTHORS.rst @@ -0,0 +1,10 @@ +Authors +======= + +Xiaohao Yang and Billinge Group members + +Contributors +------------ + +For a list of contributors, visit +https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors diff --git a/AUTHORS.txt b/AUTHORS.txt deleted file mode 100644 index f0671d8..0000000 --- a/AUTHORS.txt +++ /dev/null @@ -1 +0,0 @@ -Xiaohao Yang \ No newline at end of file diff --git a/CHANGELOG.rst b/CHANGELOG.rst new file mode 100644 index 0000000..f29d3b5 --- /dev/null +++ b/CHANGELOG.rst @@ -0,0 +1,5 @@ +============= +Release notes +============= + +.. current developments diff --git a/CODE-OF-CONDUCT.rst b/CODE-OF-CONDUCT.rst new file mode 100644 index 0000000..e8199ca --- /dev/null +++ b/CODE-OF-CONDUCT.rst @@ -0,0 +1,133 @@ +===================================== + Contributor Covenant Code of Conduct +===================================== + +Our Pledge +---------- + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socioeconomic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +Our Standards +------------- + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +Enforcement Responsibilities +---------------------------- + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders 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, and will communicate reasons for moderation +decisions when appropriate. + +Scope +----- + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +Enforcement +----------- + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +sb2896@columbia.edu. All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +Enforcement Guidelines +---------------------- + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +1. Correction +**************** + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +2. Warning +************* + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +3. Temporary Ban +****************** + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +4. Permanent Ban +****************** + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +Attribution +----------- + +This Code of Conduct is adapted from the `Contributor Covenant `_. + +Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder `_. + +For answers to common questions about this code of conduct, see the `FAQ `_. `Translations are available `_ diff --git a/DistancePrinter/__init__.py b/DistancePrinter/__init__.py deleted file mode 100644 index 5dc714a..0000000 --- a/DistancePrinter/__init__.py +++ /dev/null @@ -1,22 +0,0 @@ -#!/usr/bin/env python -############################################################################## -# -# DistancePrinter by Simon J. L. Billinge group -# (c) 2013 Trustees of the Columbia University -# in the City of New York. All rights reserved. -# -# File coded by: Xiaohao Yang -# -# See AUTHORS.txt for a list of people who contributed. -# See LICENSENOTICE.txt for license information. -# -############################################################################## - -""" -Blank namespace package. -""" - -__import__('pkg_resources').declare_namespace(__name__) - - -# End of file diff --git a/DistancePrinter/distanceprinter.py b/DistancePrinter/distanceprinter.py deleted file mode 100644 index 3a16d94..0000000 --- a/DistancePrinter/distanceprinter.py +++ /dev/null @@ -1,106 +0,0 @@ -#!/usr/bin/env python -############################################################################## -# -# DistancePrinter by Simon J. L. Billinge group -# (c) 2013 Trustees of the Columbia University -# in the City of New York. All rights reserved. -# -# File coded by: Xiaohao Yang -# -# See AUTHORS.txt for a list of people who contributed. -# See LICENSENOTICE.txt for license information. -# -############################################################################## - -import os -import sys -import itertools -import numpy as np - -from diffpy.pdffit2 import PdfFit -from diffpy.Structure import PDFFitStructure - -def calDistance(strufile, atomi, atomj, lb, ub, complete): - - stru = PDFFitStructure(filename=strufile) - pdffit = PdfFit() - pdffit.add_structure(stru) - ele = stru.element - - rv = pdffit.bond_length_types(atomi, atomj, lb, ub) - dij = np.around(rv['dij'], 6) - ddij = np.around(rv['ddij'], 10) - rv['all0ddij'] = np.all(ddij == 0) - ij0 = rv['ij0'] - - chardtype = 'S8' if complete else 'S4' - dtypec = [('distance', float), ('dd', float), ('i', chardtype), ('j', chardtype)] - distlist = np.zeros(len(dij), dtype=dtypec) - - if not complete: - for i, dist, dd, ij in itertools.izip(range(len(dij)), dij, ddij, ij0): - if ij[0] > ij[1]: - distlist[i] = (dist, dd, ele[ij[1]], ele[ij[0]]) - else: - distlist[i] = (dist, dd, ele[ij[0]], ele[ij[1]]) - distlist = np.unique(distlist) - else: - for i, dist, dd, ij in itertools.izip(range(len(dij)), dij, ddij, ij0): - distlist[i] = (dist, dd, '%s.%i' % (ele[ij[0]], ij[0]), '%s.%i' % (ele[ij[1]], ij[1])) - - distlist.sort(order='distance') - rv['distlist'] = distlist - rv['atomi'] = atomi - rv['atomj'] = atomj - rv['lb'] = lb - rv['ub'] = ub - rv['complete'] = complete - rv['stru'] = stru - rv['strufile'] = strufile - return rv - -def formatResults(stru, distlist, complete, all0ddij, **kw): - ''' - format the distlist to string - ''' - lines = [] - # header - lines.append("# Structure file: %s" % kw['strufile']) - lines.append('# ') - strustr = stru.__str__().splitlines() - lines.append('# ' + strustr[0]) - for i in range(1, len(strustr)): - lines.append('# %2i ' % (i - 1) + strustr[i]) - lines.append('# ') - lines.append('# Inter-atomic distance of (%s, %s) in (%2.2f, %2.2f) A' - % (kw['atomi'], kw['atomj'], kw['lb'], kw['ub'])) - lines.append('') - - if complete: - for dist in distlist: - lines.append('%s-%s:\t%2.6f' % (dist[2], dist[3], dist[0])) - else: - for dist in distlist: - lines.append('%s-%s:\t%2.6f (%1.1e)' % (dist[2], dist[3], dist[0], dist[1])) - rv = '\n'.join(lines) - return rv - -def writeToFile(filename, rv): - f = file(filename, 'w') - f.write(rv) - f.close() - return - -def main(): - sysargv = sys.argv[1:] - strufile, atomi, atomj, lb, ub, complete, filename = sysargv - lb = float(lb) - ub = float(ub) - complete = ('1' == complete) - rv = calDistance(strufile, atomi, atomj, lb, ub, complete) - strv = formatResults(**rv) - writeToFile(filename, strv) - return - -if __name__ == '__main__': - main() diff --git a/DistancePrinter/version.py b/DistancePrinter/version.py deleted file mode 100644 index 486d6b7..0000000 --- a/DistancePrinter/version.py +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env python -############################################################################## -# -# DistancePrinter by Simon J. L. Billinge group -# (c) 2013 Trustees of the Columbia University -# in the City of New York. All rights reserved. -# -# File coded by: Xiaohao Yang -# -# See AUTHORS.txt for a list of people who contributed. -# See LICENSENOTICE.txt for license information. -# -############################################################################## - - -"""Definition of __version__, __date__, __gitsha__. -""" - -from pkg_resources import resource_filename -from ConfigParser import RawConfigParser - -# obtain version information from the version.cfg file -cp = RawConfigParser(dict(version='', date='', commit='', timestamp=0)) -if not cp.read(resource_filename(__name__, 'version.cfg')): - from warnings import warn - warn('Package metadata not found, execute "./setup.py egg_info".') - -__version__ = cp.get('DEFAULT', 'version') -__date__ = cp.get('DEFAULT', 'date') -__gitsha__ = cp.get('DEFAULT', 'commit') -__timestamp__ = cp.getint('DEFAULT', 'timestamp') - -del cp - -# End of file diff --git a/LICENSENOTICE.txt b/LICENSENOTICE.txt index 68ada6a..c5cdb02 100644 --- a/LICENSENOTICE.txt +++ b/LICENSENOTICE.txt @@ -5,6 +5,6 @@ prohibited. If you don’t know whether or not your anticipated use is under a license, you must contact Prof. Simon Billinge at sb2896@columbia.edu. Use of this software without a license is prohibited. -Copyright 2009-2014, Trustees of Columbia University in the City of New York. +Copyright 2009-2025, Trustees of Columbia University in the City of New York. For more information please email Prof. Simon Billinge at sb2896@columbia.edu diff --git a/MANIFEST.in b/MANIFEST.in index 35a5d8c..0ecc683 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,3 +1,3 @@ recursive-include DistancePrinter * prune doc -exclude MANIFEST.in \ No newline at end of file +exclude MANIFEST.in diff --git a/README.rst b/README.rst index 0e636ba..90cf3c6 100644 --- a/README.rst +++ b/README.rst @@ -1,34 +1,102 @@ -DistancePrinter -======================================================================== +|Icon| |title|_ +=============== -Software for calculating inter-atomic distance for given structure +.. |title| replace:: diffpy.distanceprinter +.. _title: https://diffpy.github.io/diffpy.distanceprinter +.. |Icon| image:: https://avatars.githubusercontent.com/diffpy + :target: https://diffpy.github.io/diffpy.distanceprinter + :height: 100px -REQUIREMENTS ------------------------------------------------------------------------- +|PythonVersion| |PR| -The DistancePrinter requires Python 2.7 and the following software: +|Black| |Tracking| -* ``diffpy.pdffit`` +.. |Black| image:: https://img.shields.io/badge/code_style-black-black + :target: https://github.com/psf/black -INSTALLATION ------------------------------------------------------------------------- +.. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff + :target: https://github.com/diffpy/diffpy.distanceprinter/pulls -To install the DistancePrinter package: +.. |PythonVersion| image:: https://img.shields.io/badge/python-3.11%20|%203.12%20|%203.13-blue + :target: https://pypi.org/project/diffpy.distanceprinter/ - python setup.py install +.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue + :target: https://github.com/diffpy/diffpy.distanceprinter/issues -By default the files are installed in the system directories, which are -usually only writeable by the root. See the usage info "./setup.py install ---help" for options to install as a normal user under a different location. -Note that installation to non-standard directories you may require adjustments -to the PATH and PYTHONPATH environment variables. +Distance Printer, calculate the inter atomic distances. Part of xPDFsuite -CONTACTS ------------------------------------------------------------------------- +Citation +-------- -For more information on diffpy.Structure please visit the project web-page +If you use diffpy.distanceprinter in a scientific publication, we would like you to cite this package as -http://www.diffpy.org/ + Xiaohao Yang, Pavol Juhas, Christopher L. Farrow and Simon J. L. Billinge, xPDFsuite: an end-to-end + software solution for high throughput pair distribution function transformation, visualization and + analysis, arXiv 1402.3163 (2025) -or email Prof. Simon Billinge at sb2896@columbia.edu. +Installation +------------ +``diffpy.distanceprinter`` is normally installed as part of the ``xpdfsuite`` software, so please refer to the +installation instructions detailed in the ``README.rst`` file of ``xpdfsuite`` `here `_. + +Independent Installation +------------------------ +You can also install ``diffpy.distanceprinter`` independently for yourself. + +Assuming you have a wheel file in the current working directory, in an active conda environment please type + + pip install ./diffpy.distanceprinter-VERSION.whl + +where you replace VERSION with the actual version you have so the command matches the filename of the +wheel file you have. + +The commands to create and activate the conda environment with name "distanceprinter-env" is + + conda create -n distanceprinter-env python=3.13 + conda activate distanceprinter-env + +If you don't have conda installed, we recomment you install `miniconda +`_ +To install this software from a Python wheel distribution format execute + + pip install ./diffpy.distanceprinter-VERSION.whl + +If you are a developer, you can also install this package from sources. First, obtain the source archive +from `GitHub `_. +Install the packages in ``./requirements/conda.txt`` and ``./requirements/tests.txt`` +using the `--file`` command: + + conda activate distanceprinter-env + conda install --file ./requirements/conda.txt + conda install --file ./requirements/tests.txt + pip install -e . # assuming you are in the top level directory of the package + +After installing the dependencies, ``cd`` into your ``diffpy.distanceprinter`` directory +and run the following :: + + pip install . + +This package also provides command-line utilities. To check the software has been installed correctly, type :: + + diffpy.distanceprinter --version + +You can also type the following command to verify the installation. :: + + python -c "import diffpy.distanceprinter; print(diffpy.distanceprinter.__version__)" + + +To view the basic usage and available commands, type :: + + diffpy.distanceprinter -h + + +Contact +------- + +For more information on diffpy.distanceprinter please visit the project `web-page `_ or email Simon J.L. Billinge Group at sb2896@columbia.edu. + +Acknowledgements +---------------- + +``diffpy.distanceprinter`` is built and maintained with `scikit-package `_. diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..9d60f49 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,194 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = build +BASENAME = $(subst .,,$(subst $() $(),,diffpy.distanceprinter)) + +# User-friendly check for sphinx-build +ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) +$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) +endif + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/$(BASENAME).qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(BASENAME).qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/$(BASENAME)" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/$(BASENAME)" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +latexpdfja: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through platex and dvipdfmx..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." + +# Manual publishing to the gh-pages branch + +GITREPOPATH = $(shell cd $(CURDIR) && git rev-parse --git-dir) +GITREMOTE = origin +GITREMOTEURL = $(shell git config --get remote.$(GITREMOTE).url) +GITLASTCOMMIT = $(shell git rev-parse --short HEAD) + +publish: + @test -d build/html || \ + ( echo >&2 "Run 'make html' first!"; false ) + git show-ref --verify --quiet refs/heads/gh-pages || \ + git branch --track gh-pages $(GITREMOTE)/gh-pages + test -d build/gh-pages || \ + git clone -s -b gh-pages $(GITREPOPATH) build/gh-pages + cd build/gh-pages && \ + git pull $(GITREMOTEURL) gh-pages + rsync -acv --delete --exclude=.git --exclude=.rsync-exclude \ + --exclude-from=build/gh-pages/.rsync-exclude \ + --link-dest=$(CURDIR)/build/html build/html/ build/gh-pages/ + cd build/gh-pages && \ + git add --all . && \ + git diff --cached --quiet || \ + git commit -m "Sync with the source at $(GITLASTCOMMIT)." + cd build/gh-pages && \ + git push origin gh-pages diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..2be8306 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,36 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build +set SPHINXPROJ=PackagingScientificPython + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% + +:end +popd diff --git a/docs/source/_static/.placeholder b/docs/source/_static/.placeholder new file mode 100644 index 0000000..e69de29 diff --git a/docs/source/api/diffpy.distanceprinter.rst b/docs/source/api/diffpy.distanceprinter.rst new file mode 100644 index 0000000..ae0bb79 --- /dev/null +++ b/docs/source/api/diffpy.distanceprinter.rst @@ -0,0 +1,30 @@ +:tocdepth: -1 + +|title| +======= + +.. |title| replace:: diffpy.distanceprinter package + +.. automodule:: diffpy.distanceprinter + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + diffpy.distanceprinter.example_package + +Submodules +---------- + +|module| +-------- + +.. |module| replace:: diffpy.distanceprinter.example_submodule module + +.. automodule:: diffpy.distanceprinter.example_submodule + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..451aec0 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,324 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +# +# diffpy.distanceprinter documentation build configuration file, created by # noqa: E501 +# sphinx-quickstart on Thu Jan 30 15:49:41 2025. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys +import time +from importlib.metadata import version +from pathlib import Path + +# Attempt to import the version dynamically from GitHub tag. +try: + fullversion = version("diffpy.distanceprinter") +except Exception: + fullversion = "No version found. The correct version will appear in the released version." # noqa: E501 + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use Path().resolve() to make it absolute, like shown here. # noqa: E501 +# sys.path.insert(0, str(Path(".").resolve())) +sys.path.insert(0, str(Path("../..").resolve())) +sys.path.insert(0, str(Path("../../src").resolve())) + +# abbreviations +ab_authors = ( + "Xiaohao Yang, Sangjoon Lee, Simon Billinge, Billinge Group members" +) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "sphinx.ext.todo", + "sphinx.ext.viewcode", + "sphinx.ext.intersphinx", + "sphinx_rtd_theme", + "sphinx_copybutton", + "m2r", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +source_suffix = [".rst", ".md"] + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = "index" + +# General information about the project. +project = "diffpy.distanceprinter" +copyright = "%Y, The Trustees of Columbia University in the City of New York" + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. + +# The short X.Y version. +version = "".join(fullversion.split(".post")[:1]) +# The full version, including alpha/beta/rc tags. +release = fullversion + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# today = '' +today = time.strftime("%B %d, %Y", time.localtime()) +year = today.split()[-1] +# Else, today_fmt is used as the format for a strftime call. +# today_fmt = '%B %d, %Y' +# substitute YEAR in the copyright string +copyright = copyright.replace("%Y", year) + +# For sphinx_copybutton extension. +# Do not copy "$" for shell commands in code-blocks. +copybutton_prompt_text = r"^\$ " +copybutton_prompt_is_regexp = True + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ["build"] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +# default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = "sphinx" + +# A list of ignored prefixes for module index sorting. +modindex_common_prefix = ["diffpy.distanceprinter"] + +# Display all warnings for missing links. +nitpicky = True + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = "sphinx_rtd_theme" + +html_context = { + "display_github": True, + "github_user": "diffpy", + "github_repo": "diffpy.distanceprinter", + "github_version": "main", + "conf_py_path": "/docs/source/", +} + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# +html_theme_options = { + "navigation_with_keys": "true", +} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +# html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +# html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +# html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +# html_static_path = ['_static'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +# html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +# html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# html_additional_pages = {} + +# If false, no module index is generated. +# html_domain_indices = True + +# If false, no index is generated. +# html_use_index = True + +# If true, the index is split into individual pages for each letter. +# html_split_index = False + +# If true, links to the reST sources are added to the pages. +# html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +# html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Output file base name for HTML help builder. +basename = "diffpy.distanceprinter".replace(" ", "").replace(".", "") +htmlhelp_basename = basename + "doc" + + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # 'papersize': 'letterpaper', + # The font size ('10pt', '11pt' or '12pt'). + # 'pointsize': '10pt', + # Additional stuff for the LaTeX preamble. + # 'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + ( + "index", + "diffpy.distanceprinter.tex", + "diffpy.distanceprinter Documentation", + ab_authors, + "manual", + ), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# latex_use_parts = False + +# If true, show page references after internal links. +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# latex_appendices = [] + +# If false, no module index is generated. +# latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ( + "index", + "diffpy.distanceprinter", + "diffpy.distanceprinter Documentation", + ab_authors, + 1, + ) +] + +# If true, show URL addresses after external links. +# man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ( + "index", + "diffpy.distanceprinter", + "diffpy.distanceprinter Documentation", + ab_authors, + "diffpy.distanceprinter", + "One line description of project.", + "Miscellaneous", + ), +] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# texinfo_no_detailmenu = False + + +# Example configuration for intersphinx: refer to the Python standard library. +# intersphinx_mapping = {'http://docs.python.org/': None} diff --git a/docs/source/release.rst b/docs/source/release.rst new file mode 100644 index 0000000..27cd0cc --- /dev/null +++ b/docs/source/release.rst @@ -0,0 +1,5 @@ +:tocdepth: -1 + +.. index:: release notes + +.. include:: ../../CHANGELOG.rst diff --git a/news/TEMPLATE.rst b/news/TEMPLATE.rst new file mode 100644 index 0000000..790d30b --- /dev/null +++ b/news/TEMPLATE.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* diff --git a/news/doc.rst b/news/doc.rst new file mode 100644 index 0000000..35c29f4 --- /dev/null +++ b/news/doc.rst @@ -0,0 +1,24 @@ +**Added:** + +* + +**Changed:** + +* Updated from Python 2.6-2.7 to Python 3.11-3.13 +* Support ``scikit-package`` Level 5 standard (https://scikit-package.github.io/scikit-package/). + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..836946d --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,88 @@ +[build-system] +requires = ["setuptools>=62.0", "setuptools-git-versioning>=2.0"] +build-backend = "setuptools.build_meta" + +[project] +name = "diffpy.distanceprinter" +dynamic=['version', 'dependencies'] +authors = [ + { name="Simon J.L. Billinge Group", email="sb2896@columbia.edu" }, +] +maintainers = [ + { name="Simon J.L. Billinge Group", email="sb2896@columbia.edu" }, +] +description = "Distance Printer, calculate the inter atomic distances. Part of xPDFsuite" +keywords = ['diffpy', 'pdf', 'data-interpretation'] +readme = "README.rst" +requires-python = ">=3.11, <3.14" +classifiers = [ + 'Development Status :: 5 - Production/Stable', + 'Environment :: Console', + 'Intended Audience :: Developers', + 'Intended Audience :: Science/Research', + 'License :: OSI Approved :: BSD License', + 'Operating System :: MacOS :: MacOS X', + 'Operating System :: Microsoft :: Windows', + 'Operating System :: POSIX', + 'Operating System :: Unix', + 'Programming Language :: Python :: 3.11', + 'Programming Language :: Python :: 3.12', + 'Programming Language :: Python :: 3.13', + 'Topic :: Scientific/Engineering :: Physics', + 'Topic :: Scientific/Engineering :: Chemistry', +] + +[project.urls] +Homepage = "https://github.com/diffpy/diffpy.distanceprinter/" +Issues = "https://github.com/diffpy/diffpy.distanceprinter/issues/" + +[tool.setuptools-git-versioning] +enabled = true +template = "{tag}" +dev_template = "{tag}" +dirty_template = "{tag}" + +[tool.setuptools.packages.find] +where = ["src"] # list of folders that contain the packages (["."] by default) +include = ["*"] # package names should match these glob patterns (["*"] by default) +exclude = [] # exclude packages matching these glob patterns (empty by default) +namespaces = false # to disable scanning PEP 420 namespaces (true by default) + +[project.scripts] +diffpy-distanceprinter = "diffpy.distanceprinter:main" + +[tool.setuptools.dynamic] +dependencies = {file = ["requirements/pip.txt"]} + +[tool.codespell] +exclude-file = ".codespell/ignore_lines.txt" +ignore-words = ".codespell/ignore_words.txt" +skip = "*.cif,*.dat" + +[tool.docformatter] +recursive = true +wrap-summaries = 72 +wrap-descriptions = 72 + +[tool.black] +line-length = 79 +include = '\.pyi?$' +exclude = ''' +/( + \.git + | \.hg + | \.mypy_cache + | \.tox + | \.venv + | \.rst + | \.txt + | _build + | buck-out + | build + | dist + + # The following are specific to Black, you probably don't want those. + | blib2to3 + | tests/data +)/ +''' diff --git a/requirements/build.txt b/requirements/build.txt new file mode 100644 index 0000000..e69de29 diff --git a/requirements/conda.txt b/requirements/conda.txt new file mode 100644 index 0000000..92111f9 --- /dev/null +++ b/requirements/conda.txt @@ -0,0 +1,3 @@ +numpy +diffpy.pdffit2 +diffpy.structure diff --git a/requirements/docs.txt b/requirements/docs.txt new file mode 100644 index 0000000..5f34c6e --- /dev/null +++ b/requirements/docs.txt @@ -0,0 +1,5 @@ +sphinx +sphinx_rtd_theme +sphinx-copybutton +doctr +m2r diff --git a/requirements/tests.txt b/requirements/tests.txt new file mode 100644 index 0000000..a727786 --- /dev/null +++ b/requirements/tests.txt @@ -0,0 +1,6 @@ +flake8 +pytest +codecov +coverage +pytest-cov +pytest-env diff --git a/setup.py b/setup.py deleted file mode 100755 index a564855..0000000 --- a/setup.py +++ /dev/null @@ -1,114 +0,0 @@ -#!/usr/bin/env python - -# Installation script for dpx.pdfgetegui - -"""Distance Printer -""" - -import os -import glob -from setuptools import setup, find_packages - - -import os -from setuptools import setup, find_packages - -# Use this version when git data are not available, like in git zip archive. -# Update when tagging a new release. -FALLBACK_VERSION = '1.0-x' - -# versioncfgfile holds version data for git commit hash and date. -# It must reside in the same directory as version.py. -MYDIR = os.path.dirname(os.path.abspath(__file__)) -versioncfgfile = os.path.join(MYDIR, 'DistancePrinter', 'version.cfg') -gitarchivecfgfile = versioncfgfile.replace('version.cfg', 'gitarchive.cfg') - -def gitinfo(): - from subprocess import Popen, PIPE - kw = dict(stdout=PIPE, cwd=MYDIR) - proc = Popen(['git', 'describe', '--match=v[[:digit:]]*'], **kw) - desc = proc.stdout.read() - proc = Popen(['git', 'log', '-1', '--format=%H %at %ai'], **kw) - glog = proc.stdout.read() - rv = dict(version=FALLBACK_VERSION) - if desc != '': - rv['version'] = '-'.join(desc.strip().split('-')[:2]).lstrip('v') - rv['commit'], rv['timestamp'], rv['date'] = glog.strip().split(None, 2) - return rv - - -def getversioncfg(): - from ConfigParser import RawConfigParser - vd0 = dict(version=FALLBACK_VERSION, commit='', date='', timestamp=0) - # first fetch data from gitarchivecfgfile, ignore if it is unexpanded - g = vd0.copy() - cp0 = RawConfigParser(vd0) - cp0.read(gitarchivecfgfile) - if '$Format:' not in cp0.get('DEFAULT', 'commit'): - g = cp0.defaults() - # then try to obtain version data from git. - gitdir = os.path.join(MYDIR, '.git') - if os.path.isdir(gitdir) or 'GIT_DIR' in os.environ: - try: - g = gitinfo() - except OSError: - pass - # finally, check and update the active version file - cp = RawConfigParser() - cp.read(versioncfgfile) - d = cp.defaults() - rewrite = not d or (g['commit'] and ( - g['version'] != d.get('version') or g['commit'] != d.get('commit'))) - if rewrite: - cp.set('DEFAULT', 'version', g['version']) - cp.set('DEFAULT', 'commit', g['commit']) - cp.set('DEFAULT', 'date', g['date']) - cp.set('DEFAULT', 'timestamp', g['timestamp']) - cp.write(open(versioncfgfile, 'w')) - return cp - -versiondata = getversioncfg() - -# define distribution -setup_args = dict( - name='DistancePrinter', - version='1.0', - namespace_packages=['DistancePrinter'], - packages=find_packages(), - include_package_data=True, - zip_safe=False, - entry_points={ - # define console_scripts here, see setuptools docs for details. - 'console_scripts' : ['distanceprinter = DistancePrinter.distanceprinter:main' - ], - }, - - author='Simon J.L. Billinge', - author_email='sb2896@columbia.edu', - description='Distance Printer, calculate the inter atomic distance', - maintainer='Xiaohao Yang', - maintainer_email='xiaohao.yang@outlook.com', - license='see LICENSENOTICE.txt', - url='', - keywords='atomic structure', - classifiers=[ - # List of possible values at - # http://pypi.python.org/pypi?:action=list_classifiers - 'Development Status :: 5 - Production/Stable', - 'Environment :: MacOS X', - 'Environment :: Win32 (MS Windows)', - 'Environment :: X11 Applications', - 'Intended Audience :: Science/Research', - 'Operating System :: MacOS', - 'Operating System :: Microsoft :: Windows', - 'Operating System :: POSIX', - 'Programming Language :: Python :: 2.6', - 'Programming Language :: Python :: 2.7', - 'Topic :: Scientific/Engineering :: Physics', - ], -) - -if __name__ == '__main__': - setup(**setup_args) - -# End of file \ No newline at end of file diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py new file mode 100644 index 0000000..c82d1a5 --- /dev/null +++ b/src/diffpy/__init__.py @@ -0,0 +1,15 @@ +#!/usr/bin/env python +############################################################################## +# +# (c) 2013-2025 The Trustees of Columbia University in the City of New York. +# All rights reserved. +# +# File coded by: Xiaohao Yang and Billinge Group members +# +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors +# noqa: E501 +# +# See LICENSE.rst for license information. +# +############################################################################## diff --git a/src/diffpy/distanceprinter/__init__.py b/src/diffpy/distanceprinter/__init__.py new file mode 100644 index 0000000..24623df --- /dev/null +++ b/src/diffpy/distanceprinter/__init__.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python +############################################################################## +# +# (c) 2013-2025 The Trustees of Columbia University in the City of New York. +# All rights reserved. +# +# File coded by: Xiaohao Yang and Billinge Group members +# +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors +# noqa: E501 +# +# See LICENSE.rst for license information. +# +############################################################################## +"""Distance Printer, calculate the inter atomic distances. + +Part of xPDFsuite +""" + +# package version +from diffpy.distanceprinter.version import __version__ # noqa + +# silence the pyflakes syntax checker +assert __version__ or True + +# End of file diff --git a/src/diffpy/distanceprinter/distanceprinter.py b/src/diffpy/distanceprinter/distanceprinter.py new file mode 100644 index 0000000..23acd5e --- /dev/null +++ b/src/diffpy/distanceprinter/distanceprinter.py @@ -0,0 +1,152 @@ +#!/usr/bin/env python +############################################################################## +# +# (c) 2013-2025 The Trustees of Columbia University in the City of New York. +# All rights reserved. +# +# File coded by: Xiaohao Yang and Billinge Group members +# +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors +# noqa: E501 +# +# See LICENSE.rst for license information. +# +############################################################################## + +import sys + +import numpy as np + +from diffpy.pdffit2 import PdfFit +from diffpy.structure import PDFFitStructure + + +def calDistance(strufile, atomi, atomj, lb, ub, complete): + + stru = PDFFitStructure(filename=strufile) + pdffit = PdfFit() + pdffit.add_structure(stru) + ele = stru.element + + rv = pdffit.bond_length_types(atomi, atomj, lb, ub) + dij = np.around(rv["dij"], 6) + ddij = np.around(rv["ddij"], 10) + rv["all0ddij"] = np.all(ddij == 0) + ij0 = rv["ij0"] + + chardtype = "S8" if complete else "S4" + dtypec = [ + ("distance", float), + ("dd", float), + ("i", chardtype), + ("j", chardtype), + ] + distlist = np.zeros(len(dij), dtype=dtypec) + + if not complete: + for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): + if ij[0] > ij[1]: + distlist[i] = (dist, dd, ele[ij[1]], ele[ij[0]]) + else: + distlist[i] = (dist, dd, ele[ij[0]], ele[ij[1]]) + distlist = np.unique(distlist) + else: + for i, dist, dd, ij in zip(range(len(dij)), dij, ddij, ij0): + distlist[i] = ( + dist, + dd, + "%s.%i" % (ele[ij[0]], ij[0]), + "%s.%i" % (ele[ij[1]], ij[1]), + ) + + distlist.sort(order="distance") + rv["distlist"] = distlist + rv["atomi"] = atomi + rv["atomj"] = atomj + rv["lb"] = lb + rv["ub"] = ub + rv["complete"] = complete + rv["stru"] = stru + rv["strufile"] = strufile + return rv + + +def formatResults(stru, distlist, complete, all0ddij, **kw): + """Format the distlist to string.""" + lines = [] + # header + lines.append("# Structure file: %s" % kw["strufile"]) + lines.append("# ") + strustr = stru.__str__().splitlines() + lines.append("# " + strustr[0]) + for i in range(1, len(strustr)): + lines.append("# %2i " % (i - 1) + strustr[i]) + lines.append("# ") + lines.append( + "# Inter-atomic distance of (%s, %s) in (%2.2f, %2.2f) A" + % (kw["atomi"], kw["atomj"], kw["lb"], kw["ub"]) + ) + lines.append("") + + if complete: + for dist in distlist: + try: + lines.append( + "%s-%s:\t%2.6f" + % ( + dist[2].decode("utf-8"), + dist[3].decode("utf-8"), + dist[0], + ) + ) + except AttributeError: + lines.append("%s-%s:\t%2.6f" % (dist[2], dist[3], dist[0])) + else: + for dist in distlist: + try: + lines.append( + "%s-%s:\t%2.6f (%1.1e)" + % ( + dist[2].decode("utf-8"), + dist[3].decode("utf-8"), + dist[0], + dist[1], + ) + ) + except AttributeError: + lines.append( + "%s-%s:\t%2.6f (%1.1e)" + % (dist[2], dist[3], dist[0], dist[1]) + ) + rv = "\n".join(lines) + return rv + + +def writeToFile(filename, rv): + f = open(filename, "w", encoding="utf-8") + try: + rv = rv.decode("utf-8") + f.write(rv) + f.close() + except AttributeError: + # No need to decode in python 3 + f.write(rv) + f.close() + pass + + +def main(): + sysargv = sys.argv[1:] + strufile, atomi, atomj, lb, ub, complete, filename = sysargv + lb = float(lb) + ub = float(ub) + complete = "1" == complete + rv = calDistance(strufile, atomi, atomj, lb, ub, complete) + strv = formatResults(**rv) + writeToFile(filename, strv) + return + + +if __name__ == "__main__": + main() diff --git a/src/diffpy/distanceprinter/version.py b/src/diffpy/distanceprinter/version.py new file mode 100644 index 0000000..e05d9ea --- /dev/null +++ b/src/diffpy/distanceprinter/version.py @@ -0,0 +1,27 @@ +#!/usr/bin/env python +############################################################################## +# +# (c) 2013-2025 The Trustees of Columbia University in the City of New York. +# All rights reserved. +# +# File coded by: Xiaohao Yang and Billinge Group members +# +# See GitHub contributions for a more detailed list of contributors. +# https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors +# noqa: E501 +# +# See LICENSE.rst for license information. +# +############################################################################## +"""Definition of __version__.""" + +# We do not use the other three variables, but can be added back if needed. +# __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"] + +# obtain version information +from importlib.metadata import PackageNotFoundError, version + +try: + __version__ = version("diffpy.distanceprinter") +except PackageNotFoundError: + __version__ = "unknown" diff --git a/tests/data/Ni-9008476.cif b/tests/data/Ni-9008476.cif new file mode 100644 index 0000000..12aeff6 --- /dev/null +++ b/tests/data/Ni-9008476.cif @@ -0,0 +1,250 @@ +#------------------------------------------------------------------------------ +#$Date: 2017-10-15 03:23:08 +0300 (Sun, 15 Oct 2017) $ +#$Revision: 202022 $ +#$URL: file:///home/coder/svn-repositories/cod/cif/9/00/84/9008476.cif $ +#------------------------------------------------------------------------------ +# +# This file is available in the Crystallography Open Database (COD), +# http://www.crystallography.net/. The original data for this entry +# were provided the American Mineralogist Crystal Structure Database, +# http://rruff.geo.arizona.edu/AMS/amcsd.php +# +# The file may be used within the scientific community so long as +# proper attribution is given to the journal article from which the +# data were obtained. +# +data_9008476 +loop_ +_publ_author_name +'Wyckoff, R. W. G.' +_publ_section_title +; + Second edition. Interscience Publishers, New York, New York + Cubic closest packed, ccp, structure +; +_journal_name_full 'Crystal Structures' +_journal_page_first 7 +_journal_page_last 83 +_journal_volume 1 +_journal_year 1963 +_chemical_formula_sum Ni +_chemical_name_mineral Nickel +_space_group_IT_number 225 +_symmetry_space_group_name_Hall '-F 4 2 3' +_symmetry_space_group_name_H-M 'F m -3 m' +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 +_cell_length_a 3.52387 +_cell_length_b 3.52387 +_cell_length_c 3.52387 +_cell_volume 43.758 +_exptl_crystal_density_diffrn 8.909 +_cod_original_sg_symbol_H-M 'F m 3 m' +_cod_database_code 9008476 +loop_ +_symmetry_equiv_pos_as_xyz +x,y,z +x,1/2+y,1/2+z +1/2+x,y,1/2+z +1/2+x,1/2+y,z +z,-x,y +z,1/2-x,1/2+y +1/2+z,-x,1/2+y +1/2+z,1/2-x,y +-y,z,-x +-y,1/2+z,1/2-x +1/2-y,z,1/2-x +1/2-y,1/2+z,-x +x,-y,z +x,1/2-y,1/2+z +1/2+x,-y,1/2+z +1/2+x,1/2-y,z +-z,x,-y +-z,1/2+x,1/2-y +1/2-z,x,1/2-y +1/2-z,1/2+x,-y +y,-z,x +y,1/2-z,1/2+x +1/2+y,-z,1/2+x 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0.500000 0.500000 1.0000 +# 2 Ni 0.500000 0.000000 0.500000 1.0000 +# 3 Ni 0.500000 0.500000 0.000000 1.0000 +# +# Inter-atomic distance of (all, all) in (1.00, 10.00) A + +Ni.0-Ni.1: 2.491752 +Ni.0-Ni.1: 2.491752 +Ni.0-Ni.1: 2.491752 +Ni.0-Ni.1: 2.491752 +Ni.0-Ni.2: 2.491752 +Ni.0-Ni.2: 2.491752 +Ni.0-Ni.2: 2.491752 +Ni.0-Ni.2: 2.491752 +Ni.0-Ni.3: 2.491752 +Ni.0-Ni.3: 2.491752 +Ni.0-Ni.3: 2.491752 +Ni.0-Ni.3: 2.491752 +Ni.1-Ni.0: 2.491752 +Ni.1-Ni.0: 2.491752 +Ni.1-Ni.0: 2.491752 +Ni.1-Ni.0: 2.491752 +Ni.1-Ni.2: 2.491752 +Ni.1-Ni.2: 2.491752 +Ni.1-Ni.2: 2.491752 +Ni.1-Ni.2: 2.491752 +Ni.1-Ni.3: 2.491752 +Ni.1-Ni.3: 2.491752 +Ni.1-Ni.3: 2.491752 +Ni.1-Ni.3: 2.491752 +Ni.2-Ni.0: 2.491752 +Ni.2-Ni.0: 2.491752 +Ni.2-Ni.0: 2.491752 +Ni.2-Ni.0: 2.491752 +Ni.2-Ni.1: 2.491752 +Ni.2-Ni.1: 2.491752 +Ni.2-Ni.1: 2.491752 +Ni.2-Ni.1: 2.491752 +Ni.2-Ni.3: 2.491752 +Ni.2-Ni.3: 2.491752 +Ni.2-Ni.3: 2.491752 +Ni.2-Ni.3: 2.491752 +Ni.3-Ni.0: 2.491752 +Ni.3-Ni.0: 2.491752 +Ni.3-Ni.0: 2.491752 +Ni.3-Ni.0: 2.491752 +Ni.3-Ni.1: 2.491752 +Ni.3-Ni.1: 2.491752 +Ni.3-Ni.1: 2.491752 +Ni.3-Ni.1: 2.491752 +Ni.3-Ni.2: 2.491752 +Ni.3-Ni.2: 2.491752 +Ni.3-Ni.2: 2.491752 +Ni.3-Ni.2: 2.491752 +Ni.0-Ni.0: 3.523870 +Ni.0-Ni.0: 3.523870 +Ni.0-Ni.0: 3.523870 +Ni.0-Ni.0: 3.523870 +Ni.0-Ni.0: 3.523870 +Ni.0-Ni.0: 3.523870 +Ni.1-Ni.1: 3.523870 +Ni.1-Ni.1: 3.523870 +Ni.1-Ni.1: 3.523870 +Ni.1-Ni.1: 3.523870 +Ni.1-Ni.1: 3.523870 +Ni.1-Ni.1: 3.523870 +Ni.2-Ni.2: 3.523870 +Ni.2-Ni.2: 3.523870 +Ni.2-Ni.2: 3.523870 +Ni.2-Ni.2: 3.523870 +Ni.2-Ni.2: 3.523870 +Ni.2-Ni.2: 3.523870 +Ni.3-Ni.3: 3.523870 +Ni.3-Ni.3: 3.523870 +Ni.3-Ni.3: 3.523870 +Ni.3-Ni.3: 3.523870 +Ni.3-Ni.3: 3.523870 +Ni.3-Ni.3: 3.523870 +Ni.0-Ni.1: 4.315842 +Ni.0-Ni.1: 4.315842 +Ni.0-Ni.1: 4.315842 +Ni.0-Ni.1: 4.315842 +Ni.0-Ni.1: 4.315842 +Ni.0-Ni.1: 4.315842 +Ni.0-Ni.1: 4.315842 +Ni.0-Ni.1: 4.315842 +Ni.0-Ni.2: 4.315842 +Ni.0-Ni.2: 4.315842 +Ni.0-Ni.2: 4.315842 +Ni.0-Ni.2: 4.315842 +Ni.0-Ni.2: 4.315842 +Ni.0-Ni.2: 4.315842 +Ni.0-Ni.2: 4.315842 +Ni.0-Ni.2: 4.315842 +Ni.0-Ni.3: 4.315842 +Ni.0-Ni.3: 4.315842 +Ni.0-Ni.3: 4.315842 +Ni.0-Ni.3: 4.315842 +Ni.0-Ni.3: 4.315842 +Ni.0-Ni.3: 4.315842 +Ni.0-Ni.3: 4.315842 +Ni.0-Ni.3: 4.315842 +Ni.1-Ni.0: 4.315842 +Ni.1-Ni.0: 4.315842 +Ni.1-Ni.0: 4.315842 +Ni.1-Ni.0: 4.315842 +Ni.1-Ni.0: 4.315842 +Ni.1-Ni.0: 4.315842 +Ni.1-Ni.0: 4.315842 +Ni.1-Ni.0: 4.315842 +Ni.1-Ni.2: 4.315842 +Ni.1-Ni.2: 4.315842 +Ni.1-Ni.2: 4.315842 +Ni.1-Ni.2: 4.315842 +Ni.1-Ni.2: 4.315842 +Ni.1-Ni.2: 4.315842 +Ni.1-Ni.2: 4.315842 +Ni.1-Ni.2: 4.315842 +Ni.1-Ni.3: 4.315842 +Ni.1-Ni.3: 4.315842 +Ni.1-Ni.3: 4.315842 +Ni.1-Ni.3: 4.315842 +Ni.1-Ni.3: 4.315842 +Ni.1-Ni.3: 4.315842 +Ni.1-Ni.3: 4.315842 +Ni.1-Ni.3: 4.315842 +Ni.2-Ni.0: 4.315842 +Ni.2-Ni.0: 4.315842 +Ni.2-Ni.0: 4.315842 +Ni.2-Ni.0: 4.315842 +Ni.2-Ni.0: 4.315842 +Ni.2-Ni.0: 4.315842 +Ni.2-Ni.0: 4.315842 +Ni.2-Ni.0: 4.315842 +Ni.2-Ni.1: 4.315842 +Ni.2-Ni.1: 4.315842 +Ni.2-Ni.1: 4.315842 +Ni.2-Ni.1: 4.315842 +Ni.2-Ni.1: 4.315842 +Ni.2-Ni.1: 4.315842 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9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 +Ni.3-Ni.3: 9.967009 diff --git a/tests/test_distanceprinter.py b/tests/test_distanceprinter.py new file mode 100644 index 0000000..f4c987a --- /dev/null +++ b/tests/test_distanceprinter.py @@ -0,0 +1,57 @@ +import os +from io import open + +from diffpy.distanceprinter.distanceprinter import main + + +def test_distanceprinter(monkeypatch): + current_module_dir = os.path.dirname(__file__) + example_file_dir = os.path.join(current_module_dir, "data") + # must be cif, stru, or xyz file + strufile = os.path.join(example_file_dir, "Ni-9008476.cif") + # atoms typically pull from list of elements in output of PDFFitStructure. + # 'all' is always first option + atomi = "all" + atomj = "all" + # lb and ub are lower an upper bound of distance to list in angstroms + lb = 1 + ub = 10 + # 1 means keep duplicate atom pairs with same inter-atomic distance + # 0 means not to + comp = "1" + monkeypatch.setattr( + "sys.argv", + [ + "distanceprinter", + strufile, + atomi, + atomj, + lb, + ub, + comp, + "tests\\outputs\\actual.res", + ], + ) + cwd = os.getcwd() + main() + generated_file_path = os.path.join(cwd, "tests\\outputs\\actual.res") + f = open(generated_file_path, "r", encoding="utf-8") + rv0 = f.readlines() + rv0 = "".join(rv0) + resultstr = rv0 + output_file_dir = os.path.join(current_module_dir, "outputs") + example_output = os.path.join(output_file_dir, "expected.res") + f = open(example_output, "r", encoding="utf-8") + rv1 = f.readlines() + rv1 = "".join(rv1) + teststr = rv1 + + # Remove stru file path when comparing as it may differ between machines + resultstr = resultstr.split("\n", 2)[2] + teststr = teststr.split("\n", 2)[2] + + # Remove irrelevant whitespace when comparing + resultstr = "".join(resultstr.split()) + teststr = "".join(teststr.split()) + + assert resultstr == teststr diff --git a/tests/test_version.py b/tests/test_version.py new file mode 100644 index 0000000..b8b38df --- /dev/null +++ b/tests/test_version.py @@ -0,0 +1,10 @@ +"""Unit tests for __version__.py.""" + +import diffpy.distanceprinter # noqa + + +def test_package_version(): + """Ensure the package version is defined and not set to the initial + placeholder.""" + assert hasattr(diffpy.distanceprinter, "__version__") + assert diffpy.distanceprinter.__version__ != "0.0.0"