Initial commit

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Workflow files stored in the default location of `.github/workflows`
+    schedule:
+      interval: "weekly"

.github/workflows/package.yml

@@ -0,0 +1,73 @@
+name: conda packaging and deployment
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [qa, main]
+    tags: ['v*']
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          channels: conda-forge,defaults
+          use-mamba: true
+          environment-file: environment.yml
+          activate-environment: test
+      - name: install additional dependencies
+        run: |
+          echo "installing additional dependencies from environment_development.yml"
+      - name: build conda package
+        run: |
+          # set up environment
+          cd conda.recipe
+          echo "versioningit $(versioningit ../)"
+          # build the package
+          VERSION=$(versioningit ../) conda mambabuild --channel conda-forge --output-folder . .
+          conda verify noarch/mypackagename*.tar.bz2
+      - name: upload conda package to anaconda
+        shell: bash -l {0}
+        if: startsWith(github.ref, 'refs/tags/v')
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+          IS_RC: ${{ contains(github.ref, 'rc') }}
+        run: |
+          # label is main or rc depending on the tag-name
+          CONDA_LABEL="main"
+          if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
+          echo pushing ${{ github.ref }} with label $CONDA_LABEL
+          anaconda upload --label $CONDA_LABEL conda.recipe/noarch/mypackagename*.tar.bz2
+
+  pypi-publish:
+    name: upload release to PyPI
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          channels: conda-forge,defaults
+          use-mamba: true
+          environment-file: environment.yml
+          activate-environment: test
+      - name: build pypi package
+        run: |
+          # build the package
+          VERSION=$(versioningit .) python -m build
+      # publish your distributions here (need to setup on PyPI first)
+      - name: Publish package distributions to PyPI
+        if: startsWith(github.ref, 'refs/tags/v')
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/unittest.yml

@@ -0,0 +1,47 @@
+name: unit-test
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches: [next, qa, main]
+    tags: ['v*']
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          channels: conda-forge,defaults
+          use-mamba: true
+          environment-file: environment.yml
+          activate-environment: test
+      - name: install additional dependencies
+        run: |
+          echo "installing additional dependencies if cannot be installed from conda"
+      - name: run unit tests
+        run: |
+          echo "running unit tests"
+          python -m pytest --cov=src --cov-report=xml --cov-report=term-missing tests/
+      - name: upload coverage to codecov
+        uses: codecov/codecov-action@v5
+        if:
+          github.actor != 'dependabot[bot]'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+      - name: build conda package
+        run: |
+          # test that the conda package builds
+          cd conda.recipe
+          echo "versioningit $(versioningit ../)"
+          # conda channels could have been defined in the conda-incubator, but you can copy/paste the lines
+          # below to build the conda package in your local machine
+          CHANNELS="--channel mantid/label/main --channel conda-forge"
+          VERSION=$(versioningit ../) conda mambabuild $CHANNELS --output-folder . .
+          conda verify noarch/mypackagename*.tar.bz2

.gitignore

@@ -0,0 +1,161 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+.envrc

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+    - id: check-added-large-files
+      args: [--maxkb=8192]
+    - id: check-merge-conflict
+    - id: check-yaml
+      args: [--allow-multiple-documents]
+      exclude: "conda.recipe/meta.yaml"
+    - id: end-of-file-fixer
+      exclude: "tests/cis_tests/.*"
+    - id: trailing-whitespace
+      exclude: "tests/cis_tests/.*"
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.7.3
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+      exclude: "tests/cis_tests/.*"
+    - id: ruff-format
+      exclude: "tests/cis_tests/.*"
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.3.0
+  hooks:
+    - id: codespell

.readthedocs.yaml

@@ -0,0 +1,14 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "mambaforge-22.9"
+
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: true
+
+conda:
+  environment: environment.yml