lanl
diff --git a/‎.gitattributes‎
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diff --git a/‎.github/dependabot.yml‎
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diff --git a/‎.github/workflows/package.yaml‎
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diff --git a/‎.github/workflows/unittest.yaml‎
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diff --git a/‎.github/workflows/update-lockfiles.yml‎
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diff --git a/‎.gitignore‎
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diff --git a/‎.gitmodules‎
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diff --git a/‎.pixi/config.toml‎
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diff --git a/‎.pre-commit-config.yaml‎
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diff --git a/‎Notes/Pleiades.notes‎
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@@ -0,0 +1,5 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true
+
+# Do not consider Jupyter as a language
+*.ipynb linguist-vendored
@@ -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"
@@ -0,0 +1,54 @@
+name: conda packaging and deployment
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [qa, main]
+    tags: ['v*']
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.8.5
+        with:
+          pixi-version: v0.41.4
+          manifest-path: pyproject.toml
+      - name: build conda package
+        run: |
+          echo "build and verify conda package"
+          pixi run verify-conda
+      - name: upload conda package to anaconda
+        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
+          pixi run anaconda upload --label $CONDA_LABEL --user neutrons conda.recipe/noarch/mypackagename*.tar.bz2
+
+  pypi-publish:
+    name: upload release to PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.8.5
+        with:
+          pixi-version: v0.41.4
+          manifest-path: pyproject.toml
+      - name: build pypi package
+        run: |
+          # build the package
+          VERSION=$(pixi run -- versioningit .)
+          pixi run -- 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
@@ -0,0 +1,31 @@
+name: unit-test
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches: [next, qa, main]
+    tags: ['v*']
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.8.5
+        with:
+          pixi-version: v0.41.4
+          manifest-path: pyproject.toml
+      - name: run unit tests
+        run: |
+          echo "running unit tests"
+          pixi run test
+      # - 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: |
+      #     echo "build and verify conda package"
+      #     pixi run verify-conda
@@ -0,0 +1,36 @@
+name: Update lockfiles
+
+permissions:
+  contents: write
+  pull-requests: write
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: 0 5 1 * *
+
+jobs:
+  pixi-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.8.5
+        with:
+          run-install: false
+      - name: Update lockfiles
+        run: |
+          set -o pipefail
+          pixi update --json | pixi exec pixi-diff-to-markdown >> diff.md
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: Update pixi lockfile
+          title: Update pixi lockfile
+          body-path: diff.md
+          branch: update-pixi
+          base: main  # change this to the default branch of your repository
+          labels: pixi
+          delete-branch: true
+          add-paths: pixi.lock
@@ -201,3 +201,16 @@ cython_debug/
 
 # Ignore vscode stuff.
 .vscode/
+
+# Ignore development work files (use Github issues instead)
+docs/project_management
+
+# pixi environments
+.pixi
+*.egg-info
+
+# ignore versioning git files
+_version.py
+
+# ignore any scratch spaces or temporary files
+.scratch/
@@ -0,0 +1,3 @@
+[submodule "tests/data/pleiades_data"]
+	path = tests/data/pleiades_data
+	url = git@code.ornl.gov:sns-hfir-scse/infrastructure/test-data/pleiades_data.git
@@ -0,0 +1 @@
+detached-environments = true
@@ -9,20 +9,20 @@ repos:
       args: [--allow-multiple-documents]
       exclude: "conda.recipe/meta.yaml"
     - id: end-of-file-fixer
-      exclude: "nucDataLibs/.*"
+      exclude: "(tests/data/.*|legacy/.*|src/pleiades/nuclear/isotopes/files/.*|src/pleiades/nuclear/isotope/files/.*|src/pleiades/nuclear/resonances/.*)"
     - id: trailing-whitespace
-      exclude: "nucDataLibs/.*"
+      exclude: "(tests/data/.*|legacy/.*|src/pleiades/nuclear/isotopes/files/.*|src/pleiades/nuclear/isotope/files/.*|src/pleiades/nuclear/resonances/.*)"
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: v0.11.2
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
-      exclude: "nucDataLibs/.*"
+      exclude: "(tests/data/.*|legacy/.*|src/pleiades/nuclear/isotopes/files/.*|src/pleiades/nuclear/isotope/files/.*|src/pleiades/nuclear/resonances/.*)"
     - id: ruff-format
-      exclude: "nucDataLibs/.*"
+      exclude: "(tests/data/.*|legacy/.*|src/pleiades/nuclear/isotopes/files/.*|src/pleiades/nuclear/isotope/files/.*|src/pleiades/nuclear/resonances/.*)"
 - repo: https://github.com/codespell-project/codespell
   rev: v2.4.1
   hooks:
     - id: codespell
-      exclude: "(nucDataLibs/.*|.*\\.ipynb)|poetry.lock"
+      exclude: "(tests/data/.*|legacy/.*|.*\\.ipynb|pixi.lock|src/pleiades/nuclear/isotopes/files/.*|src/pleiades/nuclear/isotope/files/.*|src/pleiades/nuclear/resonances/.*|src/pleiades/sammy/alphanumerics/.*\\.(md|yaml|yml))"
       args: ["--ignore-words-list=DELTE"]
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+[submodule "tests/data/pleiades_data"]`
	`2`	`+ path = tests/data/pleiades_data`
	`3`	`+ url = git@code.ornl.gov:sns-hfir-scse/infrastructure/test-data/pleiades_data.git`