szl0072 · szl0072 · Apr 6, 2025 · Apr 6, 2025 · Apr 6, 2025 · Apr 7, 2025
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -0,0 +1,4 @@
+{
+    "name": "cclib",
+    "image": "shivupa/cclib-ci:py310-edge"
+}
diff --git a/.editorconfig b/.editorconfig
@@ -0,0 +1,17 @@
+# The full list of properties is located at
+# https://github.com/editorconfig/editorconfig/wiki/EditorConfig-Properties.
+
+root = true
+
+[*]
+charset = utf-8
+indent_size = 4
+indent_style = space
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.{yaml,yml}]
+indent_size = 2
+
+[Makefile]
+indent_style = tab
diff --git a/.envrc b/.envrc
@@ -0,0 +1 @@
+use flake .
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,26 @@
+# Psi3/Psi4: pyflakes and spacing
+fb35435f66eeb8b4825f7022cc2ab315e5379483
+## https://github.com/cclib/cclib/pull/1307
+# remove trailing whitespace
+37740d43064bc13445b19ff2d3c5f1154f202896
+# fix end of file
+8f3fbf7d1fc060a3c8522343dd103604bd946e5d
+# fix line endings to be LF
+7b2e8701dcb1a1a6c437919b185be78a35c3e2a5
+# ruff for all but cclib/parser
+e986fd9bb37ca0113707f88f6fea7f2318671cdd
+# ruff for cclib/parser
+04b3e4694e001e4b91457674a490b723e17af2b7
+# isort
+3c499da3e44e4a8ae983407c0f07c71996d202d8
+06e54bd1eb663dd948973037f336d5190f4734ce
+# pre-commit autofix
+7f407d1c7383a17cbe0995fc7bd65daf964f2eb9
+# pre-commit autofix
+0ae04b8fd098645aa3d4805abba311ccb86762dc
+# pre-commit autofix
+57041a7cd327d4206d9c870b7d37acaa556596c6
+# pre-commit autofix
+8243cb2c418f4f373c3a3e48ffa0c213dd77988e
+# pre-commit autofix
+47ee1d84e2325b15c9e5508d6d48ae1f49e507b3
diff --git a/.github/codecov.yml b/.github/codecov.yml
@@ -0,0 +1,26 @@
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+      method:
+        target: auto
+        flags:
+          - method
+      unit:
+        target: auto
+        flags:
+          - unit
+
+flags:
+  method:
+    paths:
+      - cclib/method/
+    carryforward: true
+  unit:
+    paths:
+      - cclib/io/
+      - cclib/parser/
+      - cclib/bridge/
+    carryforward: true
diff --git a/.github/license_header.txt b/.github/license_header.txt
@@ -0,0 +1,4 @@
+Copyright (c) 2024, the cclib development team
+
+This file is part of cclib (http://cclib.github.io) and is distributed under
+the terms of the BSD 3-Clause License.
diff --git a/.github/scripts/run_pytest.bash b/.github/scripts/run_pytest.bash
@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+# run_pytest.bash: Run pytest on cclib with coverage checking. Requires
+# `pytest` and `pytest-cov`.
+
+set -exo pipefail
+
+PYTEST_NWORKERS="${1}"
+
+if [[ -n "${PYTEST_NWORKERS}" ]]; then
+    PYTEST_PARALLELISM="-n ${PYTEST_NWORKERS} --dist worksteal"
+else
+    PYTEST_PARALLELISM=""
+fi
+
+if [[ "${PYTEST_ENABLE_COVERAGE}" == "true" ]]; then
+    PYTEST_COVERAGE="--cov=cclib --cov-report=term"
+else
+    PYTEST_COVERAGE=""
+fi
+
+PYTEST_ADDOPTS="-v -s ${PYTEST_PARALLELISM} ${PYTEST_COVERAGE} --cov-report=xml:coverage-unit.xml -m 'not is_method' -k 'not (data and pyscf)'" python -m pytest
+pushd data
+bash ./regression_download.sh
+popd
+PYTEST_ADDOPTS="-v -s ${PYTEST_PARALLELISM} ${PYTEST_COVERAGE} --cov-report=xml:coverage-regression.xml --cov-append" python -m pytest test/regression.py
+PYTEST_ADDOPTS="-v -s ${PYTEST_PARALLELISM} ${PYTEST_COVERAGE} --cov-report=xml:coverage-regression.xml --cov-append" python -m pytest test/regression_io.py
diff --git a/.github/scripts/run_pytest_methods.bash b/.github/scripts/run_pytest_methods.bash
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+# run_pytest.bash: Run pytest on cclib with coverage checking. Requires
+# `pytest` and `pytest-cov`.
+
+set -exo pipefail
+
+PYTEST_NWORKERS="${1}"
+
+if [[ -n "${PYTEST_NWORKERS}" ]]; then
+    PYTEST_PARALLELISM="-n ${PYTEST_NWORKERS} --dist worksteal"
+else
+    PYTEST_PARALLELISM=""
+fi
+
+if [[ "${PYTEST_ENABLE_COVERAGE}" == "true" ]]; then
+    PYTEST_COVERAGE="--cov=cclib --cov-report=term"
+else
+    PYTEST_COVERAGE=""
+fi
+
+PYTEST_ADDOPTS="-v -s ${PYTEST_PARALLELISM} ${PYTEST_COVERAGE} --cov-report=xml:coverage-method.xml -m 'is_method'" python -m pytest
diff --git a/.github/scripts/run_pytest_pyscf.bash b/.github/scripts/run_pytest_pyscf.bash
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+# run_pytest.bash: Run pytest on cclib with coverage checking. Requires
+# `pytest` and `pytest-cov`.
+
+set -exo pipefail
+
+PYTEST_NWORKERS="${1}"
+
+if [[ -n "${PYTEST_NWORKERS}" ]]; then
+    PYTEST_PARALLELISM="-n ${PYTEST_NWORKERS} --dist worksteal"
+else
+    PYTEST_PARALLELISM=""
+fi
+
+if [[ "${PYTEST_ENABLE_COVERAGE}" == "true" ]]; then
+    PYTEST_COVERAGE="--cov=cclib --cov-report=term"
+else
+    PYTEST_COVERAGE=""
+fi
+
+PYTEST_ADDOPTS="-v -s ${PYTEST_PARALLELISM} ${PYTEST_COVERAGE} --cov-report=xml:coverage-pyscf.xml -k 'data and pyscf'" python -m pytest
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,32 @@
+---
+name: ci
+
+# yamllint disable-line rule:truthy
+on:
+  push:
+  pull_request:
+
+concurrency:
+  group: ci-${{github.ref}}-${{github.event.pull_request.number || github.run_number}}
+  cancel-in-progress: true
+
+jobs:
+  prechecks:
+    uses: ./.github/workflows/pre-commit.yml
+  nix:
+    uses: ./.github/workflows/nix.yml
+  unit-tests:
+    needs: [prechecks]
+    uses: ./.github/workflows/test_and_package.yml
+  docs:
+    uses: ./.github/workflows/docs.yml
+    secrets: inherit
+  publish:
+    needs: [nix, unit-tests, docs]
+    uses: ./.github/workflows/publish.yml
+  all:
+    needs: [unit-tests, publish]
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Success
+        run: "true"
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,53 @@
+---
+# yamllint disable rule:line-length
+name: docs push
+
+# yamllint disable-line rule:truthy
+on:
+  workflow_dispatch:
+  workflow_call:
+
+concurrency:
+  group: docs-${{github.ref}}-${{github.event.pull_request.number || github.run_number}}
+  cancel-in-progress: true
+
+jobs:
+  build-and-push-docs:
+    runs-on: ubuntu-24.04
+    container:
+      image: shivupa/cclib-ci:py312-edge@sha256:1d5638793e21480301db184a5fd7b10603a19851b526af67cbb7124088dfc7c7
+    defaults:
+      run:
+        shell: bash -eo pipefail -l {0}
+    steps:
+      - name: Installs for ssh-agent
+        run: |
+          apt-get update && apt-get install -y openssh-client
+      - name: Checkout
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        with:
+          # so versioningit can figure out the version
+          fetch-depth: 0
+          fetch-tags: true
+      - name: Allow repo access (see https://github.com/actions/checkout/issues/760)
+        run: |
+          git config --global --add safe.directory /__w/cclib/cclib
+      - name: Prepare conda environment
+        run: |
+          echo "/opt/conda/envs/cclib/bin" >> "${GITHUB_PATH}"
+      - name: Build docs
+        run: cd doc && make default
+      - name: Make a no jekyll file
+        run: touch doc/sphinx/_build/html/.nojekyll
+      - name: Pushes to another repository
+        id: push_directory
+        uses: cpina/github-action-push-to-another-repository@main
+        env:
+          SSH_DEPLOY_KEY: ${{ secrets.CCLIB_DOCS_KEY }}
+        with:
+          source-directory: doc/sphinx/_build/html
+          destination-github-username: 'cclib'
+          destination-repository-name: 'cclib.github.io'
+          commit-message: See ORIGIN_COMMIT from $GITHUB_REF
+          target-branch: master
+        if: github.ref == 'refs/heads/master'
diff --git a/.github/workflows/nix.yml b/.github/workflows/nix.yml
@@ -0,0 +1,31 @@
+---
+name: build and test nix package
+
+# yamllint disable-line rule:truthy
+on:
+  workflow_dispatch:
+  workflow_call:
+
+concurrency:
+  group: nix-${{github.ref}}-${{github.event.pull_request.number || github.run_number}}
+  cancel-in-progress: true
+
+jobs:
+  nix-build:
+    runs-on: ubuntu-latest
+    steps:
+      # Install Nix on the runner
+      - uses: cachix/install-nix-action@fd24c48048070c1be9acd18c9d369a83f0fe94d7 # v31
+        with:
+          nix_path: nixpkgs=channel:nixos-unstable
+      # Pull from the cachix cache
+      - uses: cachix/cachix-action@0fc020193b5a1fa3ac4575aa3a7d3aa6a35435ad # v16
+        with:
+          name: nix-qchem
+      # Checkout of the current head in the working dir
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - name: Check nix flake
+        run: nix flake check -L
+      # Disabled until https://github.com/Nix-QChem/NixOS-QChem/issues/513 is fixed
+      # - name: Build nix package
+      #   run: nix build -L
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,25 @@
+---
+name: pre-commit
+
+# yamllint disable-line rule:truthy
+on:
+  workflow_call:
+
+concurrency:
+  group: style-${{github.ref}}-${{github.event.pull_request.number || github.run_number}}
+  cancel-in-progress: true
+
+permissions: {}
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
+      - name: install dependencies for sorting regressionfiles.yaml
+        run: |
+          python -m pip install 'ruamel.yaml'
+      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1