cryoemmonitor 0.2.10__tar.gz

cryoemmonitor-0.2.10/.bumpversion.toml

@@ -0,0 +1,14 @@
+[tool.bumpversion]
+current_version = "0.2.10"
+commit = true
+tag = true
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'
+
+[[tool.bumpversion.files]]
+filename = "src/cryoem_monitor/__init__.py"
+search = '__version__ = "{current_version}"'
+replace = '__version__ = "{new_version}"'

cryoemmonitor-0.2.10/.codecov.yaml

@@ -0,0 +1,16 @@
+coverage:
+  status:
+    project:
+      default:
+        target: 0%
+        threshold: 100%
+    patch:
+      default:
+        target: 0%
+        threshold: 100%
+
+comment:
+  layout: "diff, flags"
+  branches:
+    - main
+  after_n_builds: 2

cryoemmonitor-0.2.10/.copier-answers.yml

@@ -0,0 +1,16 @@
+# Changes here will be overwritten by Copier
+_commit: 2.1.0
+_src_path: gh:DiamondLightSource/python-copier-template
+author_email: thomas.thomas@diamond.ac.uk
+author_name: Thomas Thomas
+component_owner: group:default/sscc
+description: Electron Microscope monitoring system using prometheus
+distribution_name: cryoem-monitor
+docker: false
+docs_type: README
+git_platform: github.com
+github_org: DiamondLightSource
+package_name: cryoem-monitor
+pypi: false
+repo_name: cryoem-monitor
+type_checker: mypy

cryoemmonitor-0.2.10/.devcontainer/devcontainer.json

@@ -0,0 +1,46 @@
+// For format details, see https://containers.dev/implementors/json_reference/
+{
+    "name": "Python 3 Developer Container",
+    "build": {
+        "dockerfile": "../Dockerfile",
+        "target": "developer"
+    },
+    "remoteEnv": {
+        // Allow X11 apps to run inside the container
+        "DISPLAY": "${localEnv:DISPLAY}"
+    },
+    "customizations": {
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/venv/bin/python"
+            },
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": [
+                "ms-python.python",
+                "github.vscode-github-actions",
+                "tamasfe.even-better-toml",
+                "redhat.vscode-yaml",
+                "ryanluker.vscode-coverage-gutters",
+                "charliermarsh.ruff",
+                "ms-azuretools.vscode-docker"
+            ]
+        }
+    },
+    "features": {
+        // Some default things like git config
+        "ghcr.io/devcontainers/features/common-utils:2": {
+            "upgradePackages": false
+        }
+    },
+    "runArgs": [
+        // Allow the container to access the host X11 display and EPICS CA
+        "--net=host",
+        // Make sure SELinux does not disable with access to host filesystems like tmp
+        "--security-opt=label=disable"
+    ],
+    // Mount the parent as /workspaces so we can pip install peers as editable
+    "workspaceMount": "source=${localWorkspaceFolder}/..,target=/workspaces,type=bind",
+    // After the container is created, install the python project in editable form
+    "postCreateCommand": "pip install $([ -f dev-requirements.txt ] && echo '-c dev-requirements.txt') -e '.[dev]' && pre-commit install"
+}

cryoemmonitor-0.2.10/.github/CONTRIBUTING.md

@@ -0,0 +1,27 @@
+# Contribute to the project
+
+Contributions and issues are most welcome! All issues and pull requests are
+handled through [GitHub](https://github.com/DiamondLightSource/cryoem-monitor/issues). Also, please check for any existing issues before
+filing a new one. If you have a great idea but it involves big changes, please
+file a ticket before making a pull request! We want to make sure you don't spend
+your time coding something that might not fit the scope of the project.
+
+## Issue or Discussion?
+
+Github also offers [discussions](https://github.com/DiamondLightSource/cryoem-monitor/discussions) as a place to ask questions and share ideas. If
+your issue is open ended and it is not obvious when it can be "closed", please
+raise it as a discussion instead.
+
+## Code Coverage
+
+While 100% code coverage does not make a library bug-free, it significantly
+reduces the number of easily caught bugs! Please make sure coverage remains the
+same or is improved by a pull request!
+
+## Developer Information
+
+It is recommended that developers use a [vscode devcontainer](https://code.visualstudio.com/docs/devcontainers/containers). This repository contains configuration to set up a containerized development environment that suits its own needs.
+
+This project was created using the [Diamond Light Source Copier Template](https://github.com/DiamondLightSource/python-copier-template) for Python projects.
+
+For more information on common tasks like setting up a developer environment, running the tests, and setting a pre-commit hook, see the template's [How-to guides](https://diamondlightsource.github.io/python-copier-template/2.1.0/how-to.html).

cryoemmonitor-0.2.10/.github/actions/install_requirements/action.yml

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+name: Install requirements
+description: Install a version of python then call pip install and report what was installed
+inputs:
+  python-version:
+    description: Python version to install, default is from Dockerfile
+    default: "dev"
+  pip-install:
+    description: Parameters to pass to pip install
+    default: "$([ -f dev-requirements.txt ] && echo '-c dev-requirements.txt') -e .[dev]"
+
+runs:
+  using: composite
+  steps:
+    - name: Get version of python
+      run: |
+        PYTHON_VERSION="${{ inputs.python-version }}"
+        if [ $PYTHON_VERSION == "dev" ]; then
+          PYTHON_VERSION=$(sed -n "s/ARG PYTHON_VERSION=//p" Dockerfile)
+        fi
+        echo "PYTHON_VERSION=$PYTHON_VERSION" >> "$GITHUB_ENV"
+      shell: bash
+
+    - name: Setup python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ env.PYTHON_VERSION }}
+
+    - name: Install packages
+      run: pip install ${{ inputs.pip-install }}
+      shell: bash
+
+    - name: Report what was installed
+      run: pip freeze
+      shell: bash

cryoemmonitor-0.2.10/.github/dependabot.yml

@@ -0,0 +1,24 @@
+# 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/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"
+
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      dev-dependencies:
+        patterns:
+          - "*"

cryoemmonitor-0.2.10/.github/pages/index.html

@@ -0,0 +1,11 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+    <title>Redirecting to main branch</title>
+    <meta charset="utf-8">
+    <meta http-equiv="refresh" content="0; url=./main/index.html">
+    <link rel="canonical" href="main/index.html">
+</head>
+
+</html>

cryoemmonitor-0.2.10/.github/pages/make_switcher.py

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+import json
+import logging
+from argparse import ArgumentParser
+from pathlib import Path
+from subprocess import CalledProcessError, check_output
+
+
+def report_output(stdout: bytes, label: str) -> list[str]:
+    ret = stdout.decode().strip().split("\n")
+    print(f"{label}: {ret}")
+    return ret
+
+
+def get_branch_contents(ref: str) -> list[str]:
+    """Get the list of directories in a branch."""
+    stdout = check_output(["git", "ls-tree", "-d", "--name-only", ref])
+    return report_output(stdout, "Branch contents")
+
+
+def get_sorted_tags_list() -> list[str]:
+    """Get a list of sorted tags in descending order from the repository."""
+    stdout = check_output(["git", "tag", "-l", "--sort=-v:refname"])
+    return report_output(stdout, "Tags list")
+
+
+def get_versions(ref: str, add: str | None) -> list[str]:
+    """Generate the file containing the list of all GitHub Pages builds."""
+    # Get the directories (i.e. builds) from the GitHub Pages branch
+    try:
+        builds = set(get_branch_contents(ref))
+    except CalledProcessError:
+        builds = set()
+        logging.warning(f"Cannot get {ref} contents")
+
+    # Add and remove from the list of builds
+    if add:
+        builds.add(add)
+
+    # Get a sorted list of tags
+    tags = get_sorted_tags_list()
+
+    # Make the sorted versions list from main branches and tags
+    versions: list[str] = []
+    for version in ["master", "main"] + tags:
+        if version in builds:
+            versions.append(version)
+            builds.remove(version)
+
+    # Add in anything that is left to the bottom
+    versions += sorted(builds)
+    print(f"Sorted versions: {versions}")
+    return versions
+
+
+def write_json(path: Path, repository: str, versions: str):
+    org, repo_name = repository.split("/")
+    pages_url = f"https://{org}.github.io"
+    if repo_name != f"{org}.github.io":
+        # Only add the repo name if it isn't the source for the org pages site
+        pages_url += f"/{repo_name}"
+    struct = [
+        {"version": version, "url": f"{pages_url}/{version}/"} for version in versions
+    ]
+    text = json.dumps(struct, indent=2)
+    print(f"JSON switcher:\n{text}")
+    path.write_text(text, encoding="utf-8")
+
+
+def main(args=None):
+    parser = ArgumentParser(
+        description="Make a versions.json file from gh-pages directories"
+    )
+    parser.add_argument(
+        "--add",
+        help="Add this directory to the list of existing directories",
+    )
+    parser.add_argument(
+        "repository",
+        help="The GitHub org and repository name: ORG/REPO",
+    )
+    parser.add_argument(
+        "output",
+        type=Path,
+        help="Path of write switcher.json to",
+    )
+    args = parser.parse_args(args)
+
+    # Write the versions file
+    versions = get_versions("origin/gh-pages", args.add)
+    write_json(args.output, args.repository, versions)
+
+
+if __name__ == "__main__":
+    main()

cryoemmonitor-0.2.10/.github/workflows/_check.yml

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+on:
+  workflow_call:
+    outputs:
+      branch-pr:
+        description: The PR number if the branch is in one
+        value: ${{ jobs.pr.outputs.branch-pr }}
+
+jobs:
+  pr:
+    runs-on: "ubuntu-latest"
+    outputs:
+      branch-pr: ${{ steps.script.outputs.result }}
+    steps:
+      - uses: actions/github-script@v7
+        id: script
+        if: github.event_name == 'push'
+        with:
+          script: |
+            const prs = await github.rest.pulls.list({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              head: context.repo.owner + ':${{ github.ref_name }}'
+            })
+            if (prs.data.length) {
+              console.log(`::notice ::Skipping CI on branch push as it is already run in PR #${prs.data[0]["number"]}`)
+              return prs.data[0]["number"]
+            }

cryoemmonitor-0.2.10/.github/workflows/_dist.yml

@@ -0,0 +1,32 @@
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - name: Build sdist and wheel
+        run: >
+          export SOURCE_DATE_EPOCH=$(git log -1 --pretty=%ct) &&
+          pipx run build
+
+      - name: Upload sdist and wheel as artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - name: Check for packaging errors
+        run: pipx run twine check --strict dist/*
+
+      - name: Install produced wheel
+        uses: ./.github/actions/install_requirements
+        with:
+          pip-install: dist/*.whl

cryoemmonitor-0.2.10/.github/workflows/_release.yml

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+on:
+  workflow_call:
+
+jobs:
+  artifacts:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          merge-multiple: true
+
+      - name: Zip up docs
+        run: |
+          set -vxeuo pipefail
+          if [ -d html ]; then
+            mv html $GITHUB_REF_NAME
+            zip -r docs.zip $GITHUB_REF_NAME
+            rm -rf $GITHUB_REF_NAME
+          fi
+
+      - name: Create GitHub Release
+        # We pin to the SHA, not the tag, for security reasons.
+        # https://docs.github.com/en/actions/learn-github-actions/security-hardening-for-github-actions#using-third-party-actions
+        uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564 # v2.0.4
+        with:
+          prerelease: ${{ contains(github.ref_name, 'a') || contains(github.ref_name, 'b') || contains(github.ref_name, 'rc') }}
+          files: "*"
+          generate_release_notes: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

cryoemmonitor-0.2.10/.github/workflows/_test.yml

@@ -0,0 +1,62 @@
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        type: string
+        description: The version of python to install
+        required: true
+      runs-on:
+        type: string
+        description: The runner to run this job on
+        required: true
+    secrets:
+      CODECOV_TOKEN:
+        required: true
+
+env:
+  # https://github.com/pytest-dev/pytest/issues/2042
+  PY_IGNORE_IMPORTMISMATCH: "1"
+
+jobs:
+  run:
+    runs-on: ${{ inputs.runs-on }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - if: inputs.python-version == 'dev'
+        name: Install dev versions of python packages
+        uses: ./.github/actions/install_requirements
+
+      - if: inputs.python-version == 'dev'
+        name: Write the requirements as an artifact
+        run: pip freeze --exclude-editable > /tmp/dev-requirements.txt
+
+      - if: inputs.python-version == 'dev'
+        name: Upload dev-requirements.txt
+        uses: actions/upload-artifact@v4
+        with:
+          name: dev-requirements
+          path: /tmp/dev-requirements.txt
+
+      - if: inputs.python-version != 'dev'
+        name: Install latest versions of python packages
+        uses: ./.github/actions/install_requirements
+        with:
+          python-version: ${{ inputs.python-version }}
+          pip-install: ".[dev]"
+
+      - name: Run tests
+        run: tox -e tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          name: ${{ inputs.python-version }}/${{ inputs.runs-on }}
+          files: cov.xml
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

cryoemmonitor-0.2.10/.github/workflows/_tox.yml

@@ -0,0 +1,22 @@
+on:
+  workflow_call:
+    inputs:
+      tox:
+        type: string
+        description: What to run under tox
+        required: true
+
+
+jobs:
+  run:
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install python packages
+        uses: ./.github/actions/install_requirements
+
+      - name: Run tox
+        run: tox -e ${{ inputs.tox }}

cryoemmonitor-0.2.10/.github/workflows/ci.yml

@@ -0,0 +1,73 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  check:
+    uses: ./.github/workflows/_check.yml
+
+  lint:
+    needs: check
+    if: needs.check.outputs.branch-pr == ''
+    uses: ./.github/workflows/_tox.yml
+    with:
+      tox: pre-commit,type-checking
+
+  test:
+    needs: check
+    if: needs.check.outputs.branch-pr == ''
+    strategy:
+      matrix:
+        runs-on: ["ubuntu-latest"] # can add windows-latest, macos-latest
+        python-version: ["3.10", "3.11", "3.12"]
+        include:
+          # Include one that runs in the dev environment
+          - runs-on: "ubuntu-latest"
+            python-version: "dev"
+      fail-fast: false
+    uses: ./.github/workflows/_test.yml
+    with:
+      runs-on: ${{ matrix.runs-on }}
+      python-version: ${{ matrix.python-version }}
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  dist:
+    needs: check
+    if: needs.check.outputs.branch-pr == ''
+    uses: ./.github/workflows/_dist.yml
+  
+  release:
+    if: github.ref_type == 'tag'
+    needs: [dist]
+    uses: ./.github/workflows/_release.yml
+    permissions:
+      contents: write
+
+  publish-to-pypi:
+    if: github.ref_type == 'tag'
+    needs: [dist]
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/cryoemmonitor
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v5
+        with:
+          name: dist
+          path: dist
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true

cryoemmonitor-0.2.10/.gitignore

@@ -0,0 +1,73 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# Data 
+health_monitor_Krios4
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+**/_version.py
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+cov.xml
+.pytest_cache/
+.mypy_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# likely venv names
+.venv*
+venv*
+
+# further build artifacts
+lockfiles/
+
+# ruff cache
+.ruff_cache/
+cryoem-monitor.code-workspace

cryoemmonitor-0.2.10/.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-yaml
+      - id: check-merge-conflict
+
+  - repo: local
+    hooks:
+      - id: ruff
+        name: lint with ruff
+        language: system
+        entry: ruff check --force-exclude
+        types: [python]
+        require_serial: true
+
+      - id: ruff-format
+        name: format with ruff
+        language: system
+        entry: ruff format --force-exclude
+        types: [python]
+        require_serial: true
+
+# Type checking
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.9.0 # Released 2024-03-09
+    hooks:
+      - id: mypy
+        name: Checking types in Python scripts using MyPy
+        files: '(src|tests)/.*\.py$' # RegEx string showing directories and files to check
+        # Single quote critical due to escape character '\' used in the search string
+        # (see YAML specifications - 7.3 Flow Scalar Styles)
+
+        additional_dependencies: [
+            # Install missing stub packages
+            types-requests,
+            types-PyYAML,
+          ]

cryoemmonitor-0.2.10/.vscode/extensions.json

@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "ms-vscode-remote.remote-containers",
+    ]
+}