pg-sui 1.6.14a4__tar.gz

pg_sui-1.6.14a4/.dockerignore

@@ -0,0 +1,16 @@
+.git
+__pycache__/
+.venv/
+dist/
+build/
+*.egg-info/
+pgsui/electron/app/dist/
+.venv/
+.vscode/
+.pytest_cache/
+.codex/
+*.pyc
+*.pyo
+*.pyd
+*.egg-info/
+

pg_sui-1.6.14a4/.gitattributes

@@ -0,0 +1 @@
+*.ipynb linguist-generated

pg_sui-1.6.14a4/.github/workflows/conda.yaml

@@ -0,0 +1,147 @@
+name: conda
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+  workflow_dispatch:
+    inputs:
+      run_conda_build:
+        description: "Build and upload conda package"
+        required: false
+        default: "true"
+
+jobs:
+  tests:
+    name: Unit tests (pip)
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Clean test artifacts
+        run: rm -rf dist build .pytest_cache tmp_test_output
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install dependencies
+        env:
+          MPLCONFIGDIR: ${{ runner.temp }}/mpl
+        run: |
+          python -m pip install -U pip
+          python -m pip install ".[dev]"
+
+      - name: Run tests
+        env:
+          MPLCONFIGDIR: ${{ runner.temp }}/mpl
+        run: pytest -q
+
+  clean:
+    name: Clean conda build cache
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: conda-clean
+          create-args: >-
+            micromamba
+          init-shell: bash
+
+      - name: Clean conda build cache
+        run: |
+          micromamba clean --all --yes
+
+  conda-package:
+    name: Build conda package
+    runs-on: ${{ matrix.os }}
+    needs: [tests, clean]
+    if: |
+      startsWith(github.ref, 'refs/tags/v') ||
+      (github.event_name == 'workflow_dispatch' && github.event.inputs.run_conda_build == 'true')
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            subdir: linux-64
+          - os: macos-latest
+            subdir: osx-arm64
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      MPLCONFIGDIR: /tmp/mpl
+      # Resolve token from common secret names to avoid misconfiguration
+      UPLOAD_TOKEN: ${{ secrets.PGSUI_UPLOAD_TOKEN || secrets.CONDA_UPLOAD_TOKEN }}
+      CONDA_SUBDIR: ${{ matrix.subdir }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: conda-build
+          create-args: >-
+            python=3.11
+            pip
+            conda-build
+            anaconda-client
+            -c conda-forge
+            -c defaults
+          init-shell: bash
+          cache-environment: true
+
+      - name: Build recipe
+        env:
+          PKG_VERSION: ${{ github.ref_name }}
+        run: |
+          set -euo pipefail
+          RAW_VERSION=${PKG_VERSION:-}
+          CLEAN_VERSION=${RAW_VERSION#v}
+          # Conda versions cannot contain hyphens or plus signs; normalize to dots (e.g., v1.6.14-dev2 -> 1.6.14.dev2)
+          CLEAN_VERSION=${CLEAN_VERSION//-/.}
+          CLEAN_VERSION=${CLEAN_VERSION//+/.}
+          export PKG_VERSION=${CLEAN_VERSION:-1.6.8}
+          export SETUPTOOLS_SCM_PRETEND_VERSION=${PKG_VERSION}
+          # Help conda/jinja resolve version even if .git metadata is absent
+          export GIT_DESCRIBE_TAG=${PKG_VERSION}
+          echo "Building conda package version: ${PKG_VERSION} for ${CONDA_SUBDIR}"
+          conda build conda/recipe --output-folder conda/dist -c btmartin721 -c conda-forge -c bioconda -c pytorch -c defaults
+
+      - name: Upload conda artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: conda-packages-${{ matrix.subdir }}
+          path: |
+            conda/dist/**/*.tar.bz2
+            conda/dist/**/*.conda
+
+      - name: Verify upload token
+        run: |
+          set -euo pipefail
+          if [[ -z "${UPLOAD_TOKEN:-}" ]]; then
+            echo "No Anaconda token available. Set one of the secrets: PGSUI_UPLOAD_TOKEN, CONDA_UPLOAD_TOKEN, ANACONDA_API_TOKEN, ANACONDA_TOKEN, or ANACONDA_UPLOAD_TOKEN."
+            exit 1
+          fi
+          echo "::add-mask::${UPLOAD_TOKEN}"
+
+      - name: Publish to Anaconda
+        run: |
+          set -euo pipefail
+          mapfile -t files < <(find conda/dist -type f \( -name '*.tar.bz2' -o -name '*.conda' \))
+          if [[ ${#files[@]} -eq 0 ]]; then
+            echo "No conda artifacts found to upload."
+            exit 1
+          fi
+          anaconda -t "$UPLOAD_TOKEN" upload --label main --user btmartin721 "${files[@]}"

pg_sui-1.6.14a4/.github/workflows/docker.yaml

@@ -0,0 +1,194 @@
+name: docker
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+  workflow_dispatch:
+
+env:
+  IMAGE_NAME: btmartin721/pg-sui
+
+jobs:
+  tests:
+    name: Unit tests (pip)
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Clean test artifacts
+        run: rm -rf dist build .pytest_cache tmp_test_output
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install dependencies
+        env:
+          MPLCONFIGDIR: ${{ runner.temp }}/mpl
+        run: |
+          python -m pip install -U pip
+          python -m pip install ".[dev]"
+
+      - name: Run tests
+        env:
+          MPLCONFIGDIR: ${{ runner.temp }}/mpl
+        run: pytest -q
+
+  build:
+    name: Build Docker image
+    runs-on: ubuntu-latest
+    needs: tests
+    permissions:
+      contents: read
+      packages: write
+    env:
+      DOCKERHUB_PASSWORD: ${{ secrets.DOCKERHUB_BTMARTIN721 }}
+      DOCKERHUB_USERNAME_SECRET: ${{ secrets.DOCKERHUB_USERNAME }}
+    steps:
+      - name: Maximize disk space
+        run: |
+          set -euxo pipefail
+          echo "Disk usage before cleanup:"
+          df -h
+          sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc /opt/hostedtoolcache/CodeQL /home/linuxbrew/.linuxbrew || true
+          sudo apt-get clean
+          docker system prune -af || true
+          echo "Disk usage after cleanup:"
+          df -h
+
+      - name: Wait for PyPI publish workflow (tag pushes)
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+        env:
+          GH_TOKEN: ${{ github.token }}
+          TARGET_SHA: ${{ github.sha }}
+        run: |
+          set -euo pipefail
+
+          workflow_id=$(gh api repos/${{ github.repository }}/actions/workflows --jq '.workflows[] | select(.name=="publish-pypi") | .id' | head -n 1)
+          if [[ -z "${workflow_id:-}" ]]; then
+            echo "Could not find publish-pypi workflow id in repository workflows."
+            exit 1
+          fi
+
+          echo "Waiting for publish-pypi workflow (id: $workflow_id) to finish for SHA $TARGET_SHA"
+
+          for attempt in {1..40}; do
+            run_info=$(gh api "repos/${{ github.repository }}/actions/workflows/${workflow_id}/runs" \
+              --jq 'first(.workflow_runs[] | select(.head_sha=="'"${TARGET_SHA}"'"))')
+
+            if [[ -z "${run_info:-}" || "$run_info" == "null" ]]; then
+              echo "No matching publish-pypi run yet (attempt $attempt/40); sleeping 30s..."
+              sleep 30
+              continue
+            fi
+
+            status=$(echo "$run_info" | jq -r '.status')
+            conclusion=$(echo "$run_info" | jq -r '.conclusion // ""')
+            url=$(echo "$run_info" | jq -r '.html_url')
+
+            echo "publish-pypi workflow run: $url (status=$status, conclusion=$conclusion)"
+
+            if [[ "$status" == "completed" ]]; then
+              if [[ "$conclusion" == "success" ]]; then
+                echo "publish-pypi workflow completed successfully."
+                exit 0
+              else
+                echo "publish-pypi workflow finished with conclusion=$conclusion"
+                exit 1
+              fi
+            fi
+
+            sleep 30
+          done
+
+          echo "Timed out waiting for publish-pypi workflow to complete."
+          exit 1
+
+      - name: Resolve Docker Hub username
+        id: dockerhub-creds
+        if: github.event_name != 'pull_request'
+        run: |
+          if [[ -n "${DOCKERHUB_USERNAME_SECRET}" ]]; then
+            echo "username=${DOCKERHUB_USERNAME_SECRET}" >> "$GITHUB_OUTPUT"
+          elif [[ -n "${{ vars.DOCKERHUB_USERNAME }}" ]]; then
+            echo "username=${{ vars.DOCKERHUB_USERNAME }}" >> "$GITHUB_OUTPUT"
+          else
+            echo "username=" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+        with:
+          install: true
+          driver-opts: network=host
+
+      - name: Derive version
+        id: version
+        run: |
+          if [[ "${GITHUB_REF}" == refs/tags/v* ]]; then
+            echo "version=${GITHUB_REF_NAME#v}" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGE_NAME }}
+          tags: |
+            type=semver,pattern={{version}},value=${{ steps.version.outputs.version }},enable=${{ startsWith(github.ref, 'refs/tags/v') }}
+            type=raw,value=latest,enable=${{ startsWith(github.ref, 'refs/tags/v') }}
+            type=raw,value=pr-${{ github.event.pull_request.number }},enable=${{ github.event_name == 'pull_request' }}
+            type=ref,event=branch
+            type=sha,format=short
+
+      - name: Log in to Docker Hub
+        if: github.event_name != 'pull_request' && steps.dockerhub-creds.outputs.username != '' && env.DOCKERHUB_PASSWORD != ''
+        uses: docker/login-action@v3
+        with:
+          username: ${{ steps.dockerhub-creds.outputs.username }}
+          password: ${{ env.DOCKERHUB_PASSWORD }}
+
+      - name: Warn about missing Docker Hub credentials
+        if: github.event_name != 'pull_request' && (steps.dockerhub-creds.outputs.username == '' || env.DOCKERHUB_PASSWORD == '')
+        run: |
+          echo "Docker Hub credentials not provided; skipping login. Push will fail without credentials."
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: Dockerfile
+          # Build single-arch when loading for PRs; multi-arch only for tag pushes.
+          platforms: ${{ github.event_name == 'pull_request' && 'linux/amd64' || 'linux/amd64,linux/arm64' }}
+          push: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') && env.DOCKERHUB_PASSWORD != '' && steps.dockerhub-creds.outputs.username != '' }}
+          load: ${{ github.event_name == 'pull_request' }}
+          builder: ${{ steps.buildx.outputs.name }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          provenance: false
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Smoke test image
+        if: github.event_name == 'pull_request'
+        run: |
+          image=$(echo "${{ steps.meta.outputs.tags }}" | head -n 1)
+          docker run --rm "$image" pg-sui --help
+
+      - name: Confirm Docker image built
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+        run: 'echo "Docker image pushed with tags: ${{ steps.meta.outputs.tags }}"'

pg_sui-1.6.14a4/.github/workflows/release.yaml

@@ -0,0 +1,93 @@
+name: publish-pypi
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+  workflow_dispatch:
+
+jobs:
+  tests:
+    name: Unit tests (pip)
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Clean test artifacts
+        run: rm -rf dist build .pytest_cache tmp_test_output
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install dependencies
+        env:
+          MPLCONFIGDIR: ${{ runner.temp }}/mpl
+        run: |
+          python -m pip install -U pip
+          python -m pip install ".[dev]"
+
+      - name: Run tests
+        env:
+          MPLCONFIGDIR: ${{ runner.temp }}/mpl
+        run: pytest -q
+
+  build-and-publish:
+    runs-on: ubuntu-latest
+    needs: tests
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # setuptools-scm needs the tags
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build deps
+        run: |
+          python -m pip install -U pip
+          pip install build twine
+
+      - name: Extract version from tag
+        id: version
+        run: |
+          echo "version=${GITHUB_REF_NAME#v}" >> "$GITHUB_OUTPUT"
+          echo "Publishing PG-SUI version ${GITHUB_REF_NAME#v}"
+
+      - name: Build
+        run: |
+          rm -rf dist/
+          python -m build
+
+      - name: Publish to TestPyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        run: |
+          twine upload --non-interactive --skip-existing --repository testpypi dist/*
+
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: |
+          twine upload --non-interactive --skip-existing dist/*
+
+      - name: Create GitHub release
+        uses: softprops/action-gh-release@v1
+        with:
+          tag_name: ${{ github.ref_name }}
+          name: Release ${{ github.ref_name }}
+          body: |
+            Automated release for PG-SUI ${{ github.ref_name }}.

pg_sui-1.6.14a4/.gitignore

@@ -0,0 +1,205 @@
+# ======================================================
+# Python: bytecode / caches / compiled artifacts
+# ======================================================
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+
+# ======================================================
+# Python: packaging / build artifacts
+# ======================================================
+.Python
+*.egg-info/
+*.egg
+dist/
+conda/dist/
+conda-bld/
+*.whl
+*.manifest
+*.spec
+_version.py
+
+# ======================================================
+# Python: virtual environments
+# ======================================================
+.venv/
+.venv-test-docker/
+
+# ======================================================
+# Python: type checkers
+# ======================================================
+.mypy_cache/
+dmypy.json
+dmypy.log
+.pyre/
+.pytype/
+
+# ======================================================
+# Python: testing / coverage
+# ======================================================
+.cache/
+.pytest_cache/
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+old_tests/
+test_output/
+
+# ======================================================
+# Python / ML frameworks
+# ======================================================
+*.pt
+*.pth
+
+# ======================================================
+# Notebooks / interactive environments
+# ======================================================
+.ipynb_checkpoints/
+profile_default/
+ipython_config.py
+
+# ======================================================
+# Documentation / site builds
+# ======================================================
+# Sphinx
+docs/_build/
+docs/build/_build/
+pgsui/docs/_build/
+**/doctrees/
+*.doctree
+doctrees/
+*_build/
+.buildinfo
+
+# mkdocs
+/site
+
+# Other doc/html outputs
+html/
+*.html
+
+# ======================================================
+# Web / Node / Electron
+# ======================================================
+**/node_modules/
+pgsui/electron/app/dist/
+pgsui_electron_logs/
+.codex/
+
+# ======================================================
+# IDEs / editors
+# ======================================================
+.idea/
+.spyderproject
+.spyproject
+.ropeproject
+
+# ======================================================
+# OS / misc
+# ======================================================
+.DS_Store
+*.log
+*.zip
+
+# ======================================================
+# Framework-specific leftovers (kept from template)
+# ======================================================
+# Django
+local_settings.py
+db.sqlite3
+
+# Flask
+instance/
+.webassets-cache
+
+# Scrapy
+.scrapy
+
+# PyBuilder
+target/
+
+# ======================================================
+# Project-specific outputs
+# ======================================================
+pgsui_output/
+snpio_output/
+pgsui_*_output/
+autoencoder_*_output/
+snpio_simulated_unlinked_output/
+sim_unlinked_output/
+sim_results/
+sim_results/*
+summarize/
+simulation/
+simulation/*
+sim_results/
+*14K.vcf_output/
+
+# Training / data folders
+./training_data/
+.training_data.nosync/
+training_data_2
+training_data_2*
+
+# Other tool outputs / one-offs
+monomorphic_sites_mqc.txt
+vcf_attributes.h5
+dnasp_summary_plots.cleaned.csv
+
+# ======================================================
+# Project-specific files to ignore (one-off inputs/trees)
+# ======================================================
+DEPRECATED*.py
+BOX.vcf
+BOX2.vcf
+BOX_concat_goodOnly_N214.nex
+BOX_phylogen_dataset_output/
+box_scf.cf.tree
+partitioned_all.contree
+partitioned_all.iqtree
+coala_sims.R
+sim_treeparams.py
+simulate_rad.py
+simulate_wgs.py
+summarize_results.zsh
+run_sumstats.zsh
+run_52.zsh
+training_data/
+validation_inputs/
+validation_inputs_phylip/
+validation_inputs_phylip_max150k/
+validation_inputs.tar
+iqtree_results/
+iqtree_results_GTR/
+subset_distributions.png
+subset_dimensions.csv
+subset_filenames.txt
+subset_metadata_summary.csv
+subset_metadata.csv
+subset_phylip.tar.gz
+subset_files.zsh
+subset_phylip/
+snpio_results23*_output/
+results23_test_output/
+pgsui_validation/
+iqtree_results_unique/
+iqtree_results_GTR/
+dataset_stats_output/
+pgsui_validation.nosync/
+iqtree_results_GTR.nosync/
+iqtree_results_unique.nosync/
+summarize.nosync/
+subset_phylip.nosync/
+simulation.nosync/
+validation_inputs_phylip_max150k.nosync/
+gui_test_output/
+*.dmg
+tmp_test_output/

pg_sui-1.6.14a4/.readthedocs.yaml

@@ -0,0 +1,26 @@
+# .readthedocs.yaml
+# ReadTheDocs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html
+
+# Specify the version of the ReadTheDocs configuration file
+version: 2
+
+# Python version to use
+# Set the version of Python and other tools you might need
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.11"
+
+# Sphinx documentation options
+sphinx:
+  configuration: docs/build/conf.py
+  builder: html
+  fail_on_warning: false
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

pg_sui-1.6.14a4/.vscode/launch.json

@@ -0,0 +1,8 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "configurations": [
+        { "name": "Python Debugger: Current File with Arguments", "type": "debugpy", "request": "launch", "program": "${file}", "console": "integratedTerminal", "args": "${command:pickArgs}" },
+    ]
+}