apsbits 1.0.0rc2__tar.gz

apsbits-1.0.0rc2/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Code with explanation
+2. How to run code
+3. The error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment (please complete the following information):**
+ - OS: [e.g. Linux]
+ -  Package versions implicated in the error (torch, mdlearn versions, etc)
+
+**Additional context**
+Add any other context about the problem here.

apsbits-1.0.0rc2/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false

apsbits-1.0.0rc2/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

apsbits-1.0.0rc2/.github/ISSUE_TEMPLATE/other.md

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+---
+name: Other issue template
+about: Any issue that does not fit the other templates
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Description**

apsbits-1.0.0rc2/.github/ISSUE_TEMPLATE/question-issue-template.md

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+---
+name: Question issue template
+about: Ask a question about how to use mdlearn
+title: ''
+labels: question
+assignees: ''
+
+---
+
+**Describe the question**

apsbits-1.0.0rc2/.github/PULL_REQUEST_TEMPLATE.md

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+# Description
+
+Please include a summary of the change and (optionally) which issue is fixed. Please also include
+relevant motivation and context.
+
+Fixes # (issue)
+
+## Type of change
+
+Choose which options apply, and delete the ones which do not apply.
+
+- Bug fix (non-breaking change that fixes an issue)
+- New feature (non-breaking change that adds functionality)
+- Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- Documentation update
+- Code maintenance/cleanup

apsbits-1.0.0rc2/.github/dependabot.yml

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+# Set update schedule for GitHub Actions
+# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

apsbits-1.0.0rc2/.github/workflows/code.yml

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+name: Unit Tests & Code Coverage
+
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch: # allow manual triggering
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  lint:
+    name: Code style
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Upgrade pip & test with pre-commit
+        run: |
+          set -vxeuo pipefail
+          python -m pip install --upgrade pip
+          python -m pip install pre-commit
+          pre-commit run --all-files
+
+  test-matrix:
+    name: Python ${{ matrix.python-version }} # - Redis ${{ matrix.redis-version }}
+    runs-on: ubuntu-latest
+    needs: lint
+    strategy:
+      matrix:
+        python-version:
+          - "3.11"
+          - "3.12"
+          # - "3.13"  waiting for upstream packages
+        # redis-version:
+        #   # - "6"
+        #   - "7"
+      max-parallel: 5
+    env:
+      DISPLAY: ":99.0"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install OS libraries to test Linux PyQt apps
+        run: |
+          sudo apt update -y
+          sudo apt install -y \
+            libxcb-icccm4 \
+            libxcb-image0 \
+            libxcb-keysyms1 \
+            libxcb-randr0 \
+            libxcb-render-util0 \
+            libxcb-xinerama0 \
+            libxcb-xfixes0 \
+            libxkbcommon-x11-0 \
+            screen \
+            x11-utils \
+            xvfb
+
+      # FIXME: conflicts if redis is running on host (local runners)
+      # - name: Start Redis
+      #   uses: supercharge/redis-github-action@1.7.0
+      #   with:
+      #     redis-version: ${{ matrix.redis-version }}
+      #     redis-remove-container: true # false by default
+
+      - name: Create environment Python ${{ matrix.python-version }} # - Redis ${{ matrix.redis-version }}
+        # needed for Unpack step
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          cache-environment: true
+          cache-environment-key: env-key-${{ matrix.python-version }}
+          condarc: |
+            channels:
+              - conda-forge
+              - nodefaults
+            channel-priority: flexible
+          # environment-file: environment.yml
+          environment-name: anaconda-test-env-py-${{ matrix.python-version }} # -${{ matrix.redis-version }}
+          create-args: >-
+            coveralls
+            pytest
+            pytest-cov
+            pytest-qt
+            pytest-xvfb
+            python=${{ matrix.python-version }}
+            setuptools-scm
+            pyqt>5.15
+            pyepics
+
+      - name: Install this package with pip
+        shell: bash -l {0}
+        run: |
+          set -vxeuo pipefail
+          pip install -e .
+
+      - name: Run tests with pytest & coverage
+        shell: bash -l {0}
+        run: |
+          set -vxeuo pipefail
+          coverage run --concurrency=thread --parallel-mode -m pytest -vvv --exitfirst .
+          coverage combine
+          coverage report --precision 3
+
+      - name: Upload coverage data to coveralls.io
+        shell: bash -l {0}
+        run: |
+          set -vxeuo pipefail
+          micromamba list coveralls
+          which coveralls
+          coveralls debug
+          if [ "${GITHUB_TOKEN}" != "" ]; then
+            # only upload from GitHub runner
+            coveralls --service=github
+          else
+            echo "No credentials for upload to coveralls."
+          fi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COVERALLS_FLAG_NAME: ${{ matrix.python-version }} # -${{ matrix.redis-version }}
+          COVERALLS_PARALLEL: true
+
+      - name: IPython Startup Test
+        shell: bash -l {0}
+        run: |
+          set -vxeuo pipefail
+          ipython -c "from apsbits.demo_instrument.startup import *; RE(make_devices())"
+
+  # https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support
+  coveralls:
+    name: Report unit test coverage to coveralls
+    needs: test-matrix
+    runs-on: ubuntu-latest
+    container: python:3-slim
+
+    steps:
+      - name: Gather coverage and report to Coveralls
+        run: |
+          set -vxeuo pipefail
+          echo "Finally!"
+          pip3 install --upgrade coveralls
+          # debug mode: output prepared json and reported files list to stdout
+          # https://coveralls-python.readthedocs.io/en/latest/troubleshooting.html
+          coveralls debug
+          if [ "${GITHUB_TOKEN}" != "" ]; then
+            # only upload from GitHub runner
+            coveralls --service=github --finish
+          else
+            echo "No credentials for upload to coveralls."
+          fi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

apsbits-1.0.0rc2/.github/workflows/docs.yml

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+name: Publish Sphinx docs to GitHub Pages
+# see: https://github.com/marketplace/actions/sphinx-to-github-pages
+
+on:
+  # Build the docs on pushes to main branch, PRs to main branch, and new tags.
+  # Publish only on demand.
+  push:
+    branches:
+      - main
+    tags:
+      - '*'  # all tags
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:   # allow manual triggering
+    inputs:
+      deploy:
+        description: 'Deploy documentation'
+        type: boolean
+        required: true
+        default: false
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+
+  pages:
+    name: Publish documentation
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - name: Deploy Information
+      if: ${{ github.event.inputs.deploy }}
+      run: |
+        echo "The docs will be published from this workflow run."
+
+    - name: Install pandoc
+      run: |
+        set -vxeuo pipefail
+        sudo apt-get update
+        sudo apt-get -y install pandoc
+
+    - name: Set time zone
+      run: echo "TZ=America/Chicago" >> "$GITHUB_ENV"
+
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 # required for push to dest repo
+
+    - uses: actions/setup-python@v5
+      with:
+          python-version: "3.11"
+
+    - name: Install our package
+      run: pip install -e .[doc]
+
+    - name: Sphinx
+      id: deployment
+      run: make -C docs html
+
+    - name: Publish (push gh-pages branch) only on demand
+      uses: peaceiris/actions-gh-pages@v4
+      if: ${{ github.event.inputs.deploy }}
+      with:
+        publish_branch: gh-pages
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html
+        force_orphan: true

apsbits-1.0.0rc2/.github/workflows/init_repo.sh

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+#!/usr/bin/env bash
+
+full_name=$1
+
+echo $full_name
+
+repo=$(echo $full_name | awk -F '/' '{print $2}')
+
+# Sanitize the repo name to be a valid Python package name
+sanitized_repo=$(echo "$repo" | sed 's/[^a-zA-Z0-9_-]/_/g')
+
+original_repo="APSBITS"
+
+echo $sanitized_repo
+echo $original_repo
+
+sed -i "s/$original_repo/$sanitized_repo/g" README.md
+
+# Call the create_new_instrument function
+python3 -m apsbits.utils.create_new_instrument "${sanitized_repo}_instrument" "src/."
+
+rm -rf .github/workflows/init_repo.sh
+rm -rf .github/workflows/init_repo.yml

apsbits-1.0.0rc2/.github/workflows/init_repo.yml

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+# name: Init repo
+# on: [push]
+
+# permissions:
+#   contents: write  # Enables pushing commits back to repository
+
+# jobs:
+#   rename-project:
+#     if: ${{ github.repository != 'bcda-aps/apsbits' }}
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#         with:
+#           fetch-depth: 0
+#           ref: ${{ github.head_ref }}
+
+#       - name: Set up Python
+#         uses: actions/setup-python@v5
+#         with:
+#           python-version: '3.x'
+
+#       - name: Install dependencies
+#         run: |
+#           python -m pip install --upgrade pip
+#           pip install -e . --no-deps
+#           pip install toml pyyaml
+#       - name: Run init_repo.sh
+#         run: |
+#           set -vxeuo pipefail
+#           bash .github/workflows/init_repo.sh ${{ github.repository }}
+
+#       - uses: stefanzweifel/git-auto-commit-action@v5
+#         with:
+#           commit_message: "✅ Ready to clone and code."
+#           push_options: --force
+#           tagging_message: 'v1.0.0'

apsbits-1.0.0rc2/.github/workflows/pypi.yml

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+name: Publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+
+on:
+  # Triggers the workflow on push events but only for the main branch
+  push:
+    branches:
+      - main
+    tags:
+      - "*" # all tags
+
+permissions:
+  id-token: write
+  contents: read
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+
+      - name: Install twine
+        run: >-
+          python -m
+          pip install
+          twine
+
+      - name: Check package metadata
+        run: >-
+          twine check dist/*
+
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          # password: ${{ secrets.PYPI_API_TOKEN }}
+          verbose: true

apsbits-1.0.0rc2/.github/workflows/template_sync.yml

@@ -0,0 +1,35 @@
+name: template_sync
+
+# see: https://github.com/AndreasAugustin/actions-template-sync
+
+on:
+    # cronjob trigger
+    schedule:
+      # 12:10 AM GMT on the first day of every month
+    - cron: "10 0 1 * *"
+    # manual trigger
+    workflow_dispatch:
+
+env:
+  TEMPLATE_REPO: BCDA-APS/APSBITS
+
+jobs:
+  repo-sync:
+    if: ${{ github.repository != 'bcda-aps/apsbits' }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+
+    steps:
+      # To use this repository's private action, you must check out the repository
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT
+
+      - name: actions-template-sync
+        uses: AndreasAugustin/actions-template-sync@v2
+        with:
+          source_repo_path: ${{ env.TEMPLATE_REPO }}
+          upstream_branch: main

apsbits-1.0.0rc2/.gitignore

@@ -0,0 +1,177 @@
+# 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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+# setuptools_scm
+_version.py
+
+# Developer content
+dev_*
+
+qserver/existing_plans_and_devices.yaml
+.vscode/
+.logs/
+*.dat
+*.hdf
+
+# Local Run Engine metadata dictionary
+.re_md_dict.yml