Conda/Python Package Process Creation and CI

.github/workflows/actions.yml

@@ -0,0 +1,54 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches: [next]
+    tags: ['v*']
+
+jobs:
+  conda-build:
+      runs-on: ubuntu-latest
+      defaults:
+        run:
+          shell: bash -l {0}
+      steps:
+        - uses: actions/checkout@v4
+        - uses: mamba-org/setup-micromamba@v1
+          with:
+            environment-file: environment.yml
+            cache-environment-key: ${{ runner.os }}-env-${{ hashFiles('**/environment.yml') }}
+            cache-downloads-key: ${{ runner.os }}-downloads-${{ hashFiles('**/environment.yml') }}
+            condarc: |
+              channels:
+                - conda-forge
+                - pytorch
+                - pyg
+        - name: building python wheel
+          shell: bash -l {0}
+          run: |
+            python -m build --wheel --no-isolation
+            check-wheel-contents dist/inspired-*.whl
+        - name: build conda package
+          shell: bash -l {0}
+          run: |
+            # set up environment
+            cd conda.recipe
+            echo "versioningit $(versioningit ../)"
+            # build the package
+            CHANNELS="--channel conda-forge --channel pytorch --channel pyg"
+            VERSION=$(versioningit ../) conda mambabuild $CHANNELS --output-folder . .
+            conda verify noarch/inspired*.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/inspired*.tar.bz2

.gitignore

@@ -0,0 +1,163 @@
+# 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
+_version.py
+conda.recipe/*
+!conda.recipe/meta.yaml
+# 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

conda.recipe/meta.yaml

@@ -0,0 +1,64 @@
+# load information from pyproject.toml
+{% set pyproject = load_file_data('pyproject.toml') %}
+{% set project = pyproject.get('project', {}) %}
+{% set license = project.get('license').get('text') %}
+{% set description = project.get('description') %}
+{% set project_url = pyproject.get('project', {}).get('urls') %}
+{% set url = project_url.get('homepage') %}
+# this will get the version set by environment variable
+{% set version = environ.get('VERSION') %}
+{% set version_number = version.split('+')[0] %}
+{% set git_describe_number = environ.get('GIT_DESCRIBE_NUMBER', '0') | string %}
+
+package:
+  name: inspired
+  version: {{ version_number }}
+
+source:
+  path: ..
+
+build:
+  noarch: python
+  number: {{ git_describe_number }}
+  string: py{{py}}
+  script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv
+
+requirements:
+  host:
+    - versioningit
+    - setuptools>=42
+    - wheel
+    - python
+
+  build:
+    - setuptools>=42
+    - versioningit
+
+  run:
+    - python
+    - h5py>=3.9
+    - qtpy
+    - pyqt==5  
+    - pytorch
+    - phonopy
+    - pandas
+    - seekpath
+    - matgl
+    - chgnet
+    - pymatgen==2024.5.1
+    - spglib==2.4.0
+    - mkl==2024.0
+    - pytorch-sparse
+    - pytorch-cluster
+    - pytorch-scatter
+
+  test:
+    imports:
+      - inspired
+
+about:
+  home: {{ url }}
+  license: {{ license }}
+  license_family: MIT
+  license_file: ../LICENSE
+  summary: {{ description }}

environment.yml

@@ -0,0 +1,34 @@
+name: inspired-dev
+channels:
+  - conda-forge
+  - pytorch
+  - pyg
+dependencies:
+  - anaconda-client
+  - boa
+  - check-wheel-contents
+  - conda-build
+  - conda-verify
+  - h5py >= 3.9
+  - toml
+  - setuptools
+  - pre-commit
+  - python >= 3.9
+  - python-build
+  - pymatgen==2024.5.1
+  - spglib==2.4.0
+  - versioningit
+  - pandas
+  - pyqt==5.*
+  - qtpy
+  - phonopy
+  - seekpath
+  - matgl
+  - chgnet
+  - mkl==2024.0 # solves the pytorch error
+  - pytorch
+  - pymace
+  - pyg
+  - pytorch-sparse
+  - pytorch-cluster
+  - pytorch-scatter

pyproject.toml

@@ -0,0 +1,68 @@
+[project]
+name = "inspired"
+description = "Inelastic Neutron Scattering Prediction for Instantaneous Results and Experimental Design"
+dynamic = ["version"]
+requires-python = ">=3.9"
+dependencies = [
+    "pytorch",
+    "h5py >= 3.9",
+    "phonopy",
+    "pandas",
+    "seekpath",
+    "matgl",
+    "chgnet",
+    "qtpy",
+    "pyqt5==5.*",
+    "pymatgen==2024.5.1",
+    "spglib==2.4.0",
+    "pytorch-sparse",
+    "pytorch-cluster",
+    "pytorch-scatter"
+]
+license = { text = "GPL3.0" }
+
+[project.urls]
+homepage = "https://github.com/neutrons/inspired/"
+
+[build-system]
+requires = [
+    "setuptools",
+    "wheel",
+    "toml",
+    "versioningit"
+]
+build-backend = "setuptools.build_meta"
+
+[tool.versioningit.vcs]
+method = "git"
+default-tag = "0.2.0"
+
+[tool.versioningit.next-version]
+method = "minor"
+
+[tool.versioningit.format]
+distance = "{next_version}.dev{distance}"
+dirty = "{version}+d{build_date:%Y%m%d}"
+distance-dirty = "{next_version}.dev{distance}+d{build_date:%Y%m%d%H%M}"
+
+[tool.versioningit.write]
+file = "src/inspired/_version.py"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["*.yml","*.yaml","*.ini","*.json","*.pt","*.model","oclimax*","*.ui","M3GNet-MP-2021.2.8-PES/*"]
+
+[project.gui-scripts]
+inspired = "inspired.inspired:gui"
+
+[tool.pylint]
+max-line-length = 120
+disable = ["too-many-locals",
+           "too-many-statements",
+           "too-many-instance-attributes",
+           "too-many-arguments",
+           "duplicate-code"
+]
+extension-pkg-whitelist = ["PyQt5"]