xrpd-toolbox 0.1__tar.gz

xrpd_toolbox-0.1/.copier-answers.yml

@@ -0,0 +1,21 @@
+# Changes here will be overwritten by Copier
+_commit: 5.0.3
+_src_path: https://github.com/DiamondLightSource/python-copier-template.git
+author_email: richard.dixey@diamond.ac.uk
+author_name: Richard Dixey
+component_lifecycle: experimental
+component_owner: group:default/data-analysis
+component_type: library
+description: A repository for useful python data analysis tools for the X-ray powder
+    diffraction beamlines at Diamond Light Source
+distribution_name: xrpd-toolbox
+docker: true
+docker_debug: false
+docs_type: README
+git_platform: github.com
+github_org: DiamondLightSource
+package_name: xrpd_toolbox
+pypi: true
+repo_name: xrpd-toolbox
+strict_typing: false
+type_checker: pyright

xrpd_toolbox-0.1/.devcontainer/devcontainer.json

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+// For format details, see https://containers.dev/implementors/json_reference/
+{
+    "name": "Python 3 Developer Container",
+    "build": {
+        "dockerfile": "../Dockerfile",
+        "target": "developer",
+        "platform": "linux/amd64"
+    },
+    "remoteEnv": {
+        // Allow X11 apps to run inside the container
+        "DISPLAY": "${localEnv:DISPLAY}",
+        // Put things that allow it in the persistent cache
+        "PRE_COMMIT_HOME": "/cache/pre-commit",
+        "UV_CACHE_DIR": "/cache/uv",
+        "UV_PYTHON_CACHE_DIR": "/cache/uv-python",
+        // Make a venv that is specific for this workspace path as the cache is shared
+        "UV_PROJECT_ENVIRONMENT": "/cache/venv-for${localWorkspaceFolder}",
+        // Do the equivalent of "activate" the venv so we don't have to "uv run" everything
+        "VIRTUAL_ENV": "/cache/venv-for${localWorkspaceFolder}",
+        "PATH": "/cache/venv-for${localWorkspaceFolder}/bin:${containerEnv:PATH}"
+    },
+    "customizations": {
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                // Use the container's python by default
+                "python.defaultInterpreterPath": "/cache/venv-for${localWorkspaceFolder}/bin/python",
+                // Don't activate the venv as it is already in the PATH
+                "python.terminal.activateEnvInCurrentTerminal": false,
+                "python.terminal.activateEnvironment": false,
+                // Workaround to prevent garbled python REPL in the terminal
+                // https://github.com/microsoft/vscode-python/issues/25505
+                "python.terminal.shellIntegration.enabled": false
+            },
+            // 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"
+            ]
+        }
+    },
+    // Create the config folder for the bash-config feature and uv cache
+    "initializeCommand": "mkdir -p ${localEnv:HOME}/.config/terminal-config",
+    "runArgs": [
+        // Allow the container to access the host X11 display and EPICS CA
+        "--net=host",
+        // Make sure SELinux does not disable with access to host filesystems like tmp
+        "--security-opt=label=disable"
+    ],
+    "mounts": [
+        // Mount in the user terminal config folder so it can be edited
+        {
+            "source": "${localEnv:HOME}/.config/terminal-config",
+            "target": "/user-terminal-config",
+            "type": "bind"
+        },
+        // Keep a persistent cross container cache for uv, pre-commit, and the venvs
+        {
+            "source": "devcontainer-shared-cache",
+            "target": "/cache",
+            "type": "volume"
+        },
+        {
+            "source": "${localEnv:HOME}${localEnv:USERPROFILE}",
+            "target": "/host-home",
+            "type": "bind"
+        },
+        // Mount facility directories if present on the host (Docker will create
+        // the host directory if it does not exist). These ensure /dls and
+        // /dls_sw are available inside the container when present on the host.
+        // {
+        //     "source": "/dls/i15-1/data",
+        //     "target": "/dls/i15-1/data",
+        //     "type": "bind"
+        // },
+        // {
+        //     "source": "/dls_sw",
+        //     "target": "/dls_sw",
+        //     "type": "bind"
+        // }
+    ],
+    // 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, recreate the venv then make pre-commit first run faster
+    "postCreateCommand": "uv venv --clear && uv sync && pre-commit install --install-hooks"
+}

xrpd_toolbox-0.1/.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/xrpd-toolbox/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/xrpd-toolbox/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/5.0.3/how-to.html).

xrpd_toolbox-0.1/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,21 @@
+---
+name: Bug Report
+about: The template to use for reporting bugs and usability issues
+title: " "
+labels: 'bug'
+assignees: ''
+
+---
+
+Describe the bug, including a clear and concise description of the expected behaviour, the actual behavior and the context in which you encountered it (ideally include details of your environment).
+
+## Steps To Reproduce
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+
+## Acceptance Criteria
+- Specific criteria that will be used to judge if the issue is fixed

xrpd_toolbox-0.1/.github/ISSUE_TEMPLATE/issue.md

@@ -0,0 +1,13 @@
+---
+name: Issue
+about: The standard template to use for feature requests, design discussions and tasks
+title: " "
+labels: ''
+assignees: ''
+
+---
+
+A brief description of the issue, including specific stakeholders and the business case where appropriate
+
+## Acceptance Criteria
+- Specific criteria that will be used to judge if the issue is fixed

xrpd_toolbox-0.1/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -0,0 +1,8 @@
+Fixes #ISSUE
+
+### Instructions to reviewer on how to test:
+1. Do thing x
+2. Confirm thing y happens
+
+### Checks for reviewer
+- [ ] Would the PR title make sense to a user on a set of release notes

xrpd_toolbox-0.1/.github/pages/index.html

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+<!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>

xrpd_toolbox-0.1/.github/pages/make_switcher.py

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+"""Make switcher.json to allow docs to switch between different versions."""
+
+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]:
+    """Print and return something received frm stdout."""
+    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: list[str]):
+    """Write the JSON switcher to path."""
+    org, repo_name = repository.split("/")
+    struct = [
+        {"version": version, "url": f"https://{org}.github.io/{repo_name}/{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):
+    """Parse args and write switcher."""
+    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()

xrpd_toolbox-0.1/.github/workflows/_container.yml

@@ -0,0 +1,68 @@
+on:
+  workflow_call:
+    inputs:
+      publish:
+        type: boolean
+        description: If true, pushes image to container registry
+
+permissions:
+  contents: read
+  packages: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GitHub Docker Registry
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and export to Docker local cache
+        uses: docker/build-push-action@v6
+        env:
+          DOCKER_BUILD_RECORD_UPLOAD: false
+        with:
+          context: .
+          # Need load and tags so we can test it below
+          load: true
+          tags: tag_for_testing
+
+      - name: Test cli works in cached runtime image
+        run: docker run --rm tag_for_testing --version
+
+      - name: Create tags for publishing image
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository }}
+          tags: |
+            type=ref,event=tag
+            type=raw,value=latest
+
+      - name: Push cached image to container registry
+        if: inputs.publish && github.ref_type == 'tag'
+        uses: docker/build-push-action@v6
+        env:
+          DOCKER_BUILD_RECORD_UPLOAD: false
+        # This does not build the image again, it will find the image in the
+        # Docker cache and publish it
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

xrpd_toolbox-0.1/.github/workflows/_dist.yml

@@ -0,0 +1,37 @@
+on:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Build sdist and wheel
+        run: >
+          export SOURCE_DATE_EPOCH=$(git log -1 --pretty=%ct) &&
+          uvx --from build pyproject-build
+
+      - name: Upload sdist and wheel as artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist
+
+      - name: Check for packaging errors
+        run: uvx twine check --strict dist/*
+
+      - name: Install produced wheel
+        run: python -m pip install dist/*.whl
+
+      - name: Test module --version works using the installed wheel
+        # If more than one module in src/ replace with module name to test
+        run: python -m $(ls --hide='*.egg-info' src | head -1) --version

xrpd_toolbox-0.1/.github/workflows/_pypi.yml

@@ -0,0 +1,19 @@
+on:
+  workflow_call:
+
+jobs:
+  upload:
+    runs-on: ubuntu-latest
+    environment: release
+
+    steps:
+      - name: Download dist artifact
+        uses: actions/download-artifact@v5
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to PyPI using trusted publishing
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          attestations: false

xrpd_toolbox-0.1/.github/workflows/_release.yml

@@ -0,0 +1,32 @@
+on:
+  workflow_call:
+
+jobs:
+  artifacts:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v5
+        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@6da8fa9354ddfdc4aeace5fc48d7f679b5214090 # v2.4.1
+        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 }}

xrpd_toolbox-0.1/.github/workflows/_test.yml

@@ -0,0 +1,39 @@
+on:
+  workflow_call:
+    inputs:
+      python-version:
+        type: string
+        description: The version of python to install, default is from .python-version file
+        default: ""
+      runs-on:
+        type: string
+        description: The runner to run this job on
+        required: true
+
+env:
+  # https://github.com/pytest-dev/pytest/issues/2042
+  PY_IGNORE_IMPORTMISMATCH: "1"
+  UV_PYTHON: ${{ inputs.python-version }}
+
+jobs:
+  run:
+    runs-on: ${{ inputs.runs-on }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+        with:
+          # Need this to get version number from last tag
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Run tests
+        run: uv run --locked tox -e tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          name: ${{ inputs.python-version }}/${{ inputs.runs-on }}
+          files: cov.xml

xrpd_toolbox-0.1/.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@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Run tox
+        run: uv run --locked tox -e ${{ inputs.tox }}

xrpd_toolbox-0.1/.github/workflows/ci.yml

@@ -0,0 +1,54 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+  pull_request:
+
+jobs:
+
+  lint:
+    uses: ./.github/workflows/_tox.yml
+    with:
+      tox: pre-commit,type-checking
+
+  test:
+    strategy:
+      matrix:
+        runs-on: ["ubuntu-latest"] # can add windows-latest, macos-latest
+        python-version: ["3.11", "3.12", "3.13"]
+      fail-fast: false
+    uses: ./.github/workflows/_test.yml
+    with:
+      runs-on: ${{ matrix.runs-on }}
+      python-version: ${{ matrix.python-version }}
+
+  container:
+    needs: test
+    if: always()
+    uses: ./.github/workflows/_container.yml
+    with:
+      publish: ${{ needs.test.result == 'success' }}
+    permissions:
+      contents: read
+      packages: write
+
+  dist:
+    uses: ./.github/workflows/_dist.yml
+  
+  pypi:
+    needs: [dist, test]
+    if: github.ref_type == 'tag'
+    uses: ./.github/workflows/_pypi.yml
+    permissions:
+      id-token: write
+  
+  release:
+    needs: [dist, test]
+    if: github.ref_type == 'tag'
+    uses: ./.github/workflows/_release.yml
+    permissions:
+      contents: write

xrpd_toolbox-0.1/.gitignore

@@ -0,0 +1,84 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+#h5 files, but not hdf5
+*.h5 
+
+# output of running reduction
+*.xye
+**/processed/
+
+#binary files used for ang cal
+*.obj
+
+# 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/
+docs/_api
+
+# PyBuilder
+target/
+
+# likely venv names
+.venv*
+venv*
+
+# further build artifacts
+lockfiles/
+
+# ruff cache
+.ruff_cache/
+
+#mac items
+*.DS_Store

xrpd_toolbox-0.1/.gitleaks.toml

@@ -0,0 +1,19 @@
+# This allow-list is limited to YAML/YML files to cut down SealedSecrets false positives.
+# All gitleaks default rules still apply everywhere (useDefault = true).
+# To broaden this allow-list to all files, comment out the 'paths' line below.
+
+[extend]
+useDefault = true
+
+[[rules]]
+id = "generic-api-key"
+
+# Pattern-only allowlist for long Ag… tokens in YAML 
+[[rules.allowlists]]
+condition = "AND"
+regexes = [
+  # Boundary-safe Ag… token without lookarounds (RE2-safe)
+  '''(?:^|[^A-Za-z0-9+/=])(Ag[A-Za-z0-9+/]{500,}={0,2})(?:[^A-Za-z0-9+/=]|$)'''
+]
+# Limit to YAML only for now. Comment this out if you want it to apply everywhere.
+paths = ['''(?i).*\.ya?ml$''']