pysrim2 0.6.0__tar.gz

pysrim2-0.6.0/.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# style: format with ruff
+935df1e6e25015c9a72ca8d449b1e85e98fe3e76

pysrim2-0.6.0/.gitattributes

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+# SRIM fixtures are CRLF and read byte-for-byte on every platform; never normalise them.
+test_files/** -text
+examples/input/** -text
+*.IN -text

pysrim2-0.6.0/.github/workflows/ci.yml

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+name: ci
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
+jobs:
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+
+      - name: Run pre-commit on all files
+        run: uv run --group dev pre-commit run --all-files --show-diff-on-failure
+
+  test:
+    name: test
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.11", "3.12", "3.13", "3.14", "3.15"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+
+      - name: Run tests with coverage
+        shell: bash
+        env:
+          PYTHON_VERSION: ${{ matrix.python }}
+        run: |
+          uv run --python "$PYTHON_VERSION" pytest --cov=srim --cov-report=xml --cov-fail-under=70
+
+  build:
+    name: build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+
+      - name: Build sdist and wheel
+        run: uv build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: dist
+          path: dist/
+          if-no-files-found: error

pysrim2-0.6.0/.github/workflows/release.yml

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+name: release
+
+on:
+  push:
+    tags: ["v*"]
+  workflow_dispatch:
+    inputs:
+      testpypi:
+        description: "Publish the build to TestPyPI"
+        type: boolean
+        default: true
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@1c37ad07a6a961277cf70c0d37d6f313000f5884 # v10.3.0
+
+      - name: Verify tag matches project version
+        if: github.ref_type == 'tag'
+        env:
+          TAG: ${{ github.ref_name }}
+        run: |
+          version="$(uv version --short --frozen)"
+          if [ "$TAG" != "v${version}" ]; then
+            echo "Tag '$TAG' does not match project version 'v${version}'." >&2
+            exit 1
+          fi
+          echo "Tag '$TAG' matches project version '${version}'."
+
+      - name: Build sdist and wheel
+        run: uv build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: dist
+          path: dist/
+          if-no-files-found: error
+
+  publish-testpypi:
+    needs: build
+    if: github.event_name == 'workflow_dispatch' && inputs.testpypi
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/pysrim2
+    permissions:
+      id-token: write
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    needs: build
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pysrim2
+    permissions:
+      id-token: write
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2
+
+  github-release:
+    needs: publish-pypi
+    if: github.event_name == 'push' && github.ref_type == 'tag'
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    env:
+      GH_TOKEN: ${{ github.token }}
+      TAG: ${{ github.ref_name }}
+      REPO: ${{ github.repository }}
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+
+      - name: Download distributions
+        uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
+        with:
+          name: dist
+          path: dist/
+
+      - name: Create GitHub release
+        run: |
+          version="${TAG#v}"
+          header="## [${version}]"
+          notes="notes.md"
+
+          # Extract the CHANGELOG section for this version, if there is one.
+          # Matching is literal (index), anchored at the start of the line.
+          : > "$notes"
+          if [ -f CHANGELOG.md ]; then
+            awk -v header="$header" '
+              index($0, header) == 1 { found = 1; next }
+              found && /^## \[/ { exit }
+              found && /^\[[^]]+\]: / { exit }
+              found { print }
+            ' CHANGELOG.md > "$notes"
+          fi
+
+          # Fall back to GitHub-generated notes when there is no usable section.
+          notes_args=(--generate-notes)
+          if grep -q '[^[:space:]]' "$notes"; then
+            notes_args=(--notes-file "$notes")
+          fi
+
+          prerelease_flag=()
+          if echo "$version" | grep -qE '(a|b|rc|dev)[0-9]+'; then
+            prerelease_flag=(--prerelease)
+          fi
+
+          gh release create "$TAG" dist/* \
+            --repo "$REPO" \
+            --verify-tag \
+            --title "$TAG" \
+            "${notes_args[@]}" \
+            "${prerelease_flag[@]}"

pysrim2-0.6.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+#Ipython Notebook
+.ipynb_checkpoints
+
+# pyenv
+venv
+
+# pytest
+.pytest_cache.DS_Store
+.venv/
+.superpowers/

pysrim2-0.6.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.17.3
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: end-of-file-fixer
+        # SRIM fixtures are CRLF and byte-exact; never rewrite them.
+        exclude: ^test_files/|\.IN$|^examples/input/|\.ipynb$
+      - id: trailing-whitespace
+        exclude: ^test_files/|\.IN$|^examples/input/|\.ipynb$
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+        args: [--maxkb=1024]
+
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.13.7
+    hooks:
+      - id: uv-lock

pysrim2-0.6.0/.python-version

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+3.13

pysrim2-0.6.0/.readthedocs.yaml

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+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+  jobs:
+    pre_create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    create_environment:
+      - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
+    install:
+      - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen --group docs
+
+sphinx:
+  configuration: docs/conf.py
+  fail_on_warning: true

pysrim2-0.6.0/AGENTS.md

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+# AGENTS.md
+
+pysrim2 is a maintained continuation of pysrim (distribution `pysrim2`, import `srim`).
+
+## Commands
+
+- Setup: `uv sync`
+- Test: `uv run pytest` (run from the repository root; tests use relative paths such as `test_files/`)
+- Lint and format: `uv run pre-commit run --all-files`
+- Docs: `uv run --group docs sphinx-build -W -b html docs <output dir>`
+- Build: `uv build`
+- Once per clone: `git config blame.ignoreRevsFile .git-blame-ignore-revs`
+
+## Conventions
+
+- Conventional commit prefixes (feat, fix, test, build, docs, chore, style, ci); one concern per commit.
+- Every user-visible change adds a line under `## [Unreleased]` in `CHANGELOG.md`.
+- Never commit SRIM binaries or large outputs.
+- Fixtures in `test_files/` are byte-exact SRIM output with CRLF line endings. Do not reformat them or let an editor change line endings.
+- Fork commits: bring them in with `git cherry-pick -x` so author and message are kept. Never squash or amend them. Put our own changes (tests, adjustments, credit for others who fixed the same thing via `Co-authored-by:`) in separate follow-up commits. Record the result in `docs/changes-from-pysrim.md`.
+- Python 3.11 or newer; runtime dependencies are numpy, pyyaml and pandas.

pysrim2-0.6.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.6.0] - 2026-11-03
+
+Changes since pysrim 0.5.10. See
+[changes from pysrim](https://pysrim2.readthedocs.io/en/latest/changes-from-pysrim.html) for credits and details.
+
+### Added
+
+- Run SRIM under `xvfb-run -a` when it is available, so no display is needed (Jan Mayer).
+- Parse SRIM output written with comma decimal separators (philis-johan, MrRobot2211).
+- Support the `m` (metre) length unit in SR output (Angus Hollands).
+- `SRIMOutputParseError` for unknown units in SR output.
+- GitHub Actions: lint, test matrix (Python 3.11 to 3.15 on Linux, Windows and macOS), build, and a trusted-publishing release workflow.
+- Ruff configuration and pre-commit hooks.
+- Documentation: change list relative to pysrim, changelog page, `AGENTS.md`.
+
+### Changed
+
+- The distribution is renamed to `pysrim2`; the import name `srim` is unchanged. It cannot be installed alongside `pysrim`.
+- Requires Python 3.11 or newer.
+- Packaging uses `pyproject.toml`, hatchling and uv (Angus Hollands).
+- Wine is detected with `shutil.which` through a shared launch helper (Mirochill).
+- Code formatted with ruff.
+- Documentation uses the furo theme, is built with uv, and is hosted at <https://pysrim2.readthedocs.io>.
+- README and installation instructions rewritten for pysrim2.
+
+### Fixed
+
+- Removed the `distutils` import so the package imports on Python 3.12 and later (lievcm).
+- Regular expressions use raw strings, removing invalid escape sequence warnings (lievcm).
+- Ion energies with a leading or trailing decimal point (such as `.3 keV`) are parsed (Mirochill, George Apostolopoulos, SimonF24).
+- Positive `autosave` intervals are accepted (Mirochill).
+- The sputtered output setting is honoured independently of ranges (Mirochill).
+- The element database file is closed after loading.
+- Undefined names: the `NotImpementedError` typo in `SRIM_Output._read_target`, and missing `numpy` import and `folder` argument in `srim.plot`.
+- Plot functions read `Results` attributes instead of subscripting `Results`.
+- Docstring markup errors that produced Sphinx warnings.
+
+### Removed
+
+- Support for Python versions before 3.11.
+- `setup.py`, `setup.cfg`, the conda recipe, `install.sh`, `default.nix`, GitLab CI and the old Dockerfiles. A container image and a SRIM installer for wine are planned.
+
+Versions up to and including 0.5.10 were released as `pysrim` by Chris Ostrouchov.
+
+[Unreleased]: https://github.com/FSIBT/pysrim2/compare/v0.6.0...HEAD
+[0.6.0]: https://github.com/FSIBT/pysrim2/compare/0421575...v0.6.0

pysrim2-0.6.0/CLAUDE.md

@@ -0,0 +1 @@
+@AGENTS.md

pysrim2-0.6.0/CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+education, socio-economic status, nationality, personal appearance, race,
+religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+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, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org

pysrim2-0.6.0/LICENSE

@@ -0,0 +1,23 @@
+The MIT License
+===============
+
+Copyright (c) 2018 Chris Ostrouchov
+Copyright (c) 2026 pysrim2 contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.