updated files to latest skeleton (#198)

* updated files to latest skeleton

* added main.py because versioning makes sense

* ignoring _version.py file and excluding it from black checks

* got rid of reference to requirements.txt in Dockerfile

* removed now redundant _version_git.py, changed dockerfile to inspect github CI build

* modified code to not use _version_git.py

* investigating docker error

* container is just listing its directory now

* Add experimental ls to debug ci

* Restore Docker build behavoir

* Remove dockerignore

* changed main file to take version arg

* added arg PIP_OPTIONS to be overwritten by code container CI job

* changed CMD to ENTRYPOINT in dockerfile

* removed container yml job as it is a duplication of an existing job in code yml workflow

* updated pyproject toml to look at correct version of diffcalc-core

* modified test

---------

Co-authored-by: Callum Forrester <[email protected]>

Author: rosesyrett

.devcontainer/Dockerfile

@@ -0,0 +1,21 @@
+# See here for image contents: https://github.com/microsoft/vscode-dev-containers/tree/v0.241.1/containers/python-3/.devcontainer/base.Dockerfile
+# FROM ubuntu:latest
+# [Choice] Python version (use -bullseye variants on local arm64/Apple Silicon): 3, 3.10, 3.9, 3.8, 3.7, 3.6, 3-bullseye, 3.10-bullseye, 3.9-bullseye, 3.8-bullseye, 3.7-bullseye, 3.6-bullseye, 3-buster, 3.10-buster, 3.9-buster, 3.8-buster, 3.7-buster, 3.6-buster
+ARG VARIANT="3.10-bullseye"
+FROM mcr.microsoft.com/vscode/devcontainers/python:0-${VARIANT}
+
+# # [Choice] Node.js version: none, lts/*, 16, 14, 12, 10
+ARG NODE_VERSION="none"
+RUN if [ "${NODE_VERSION}" != "none" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# [Optional] If your pip requirements rarely change, uncomment this section to add them to the image.
+# COPY requirements.txt /tmp/pip-tmp/
+# RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/requirements.txt \
+#    && rm -rf /tmp/pip-tmp
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+# [Optional] Uncomment this line to install global node packages.
+# RUN su vscode -c "source /usr/local/share/nvm/nvm.sh && npm install -g <your-package-here>" 2>&1

.devcontainer/devcontainer.json

@@ -0,0 +1,52 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.241.1/containers/python-3
+{
+    "name": "Python 3",
+    "runArgs": [
+        "--net",
+        "host"
+    ],
+    "build": {
+        "dockerfile": "Dockerfile",
+        "context": "..",
+        "args": {
+            // Update 'VARIANT' to pick a Python version: 3, 3.10, 3.9, 3.8, 3.7, 3.6
+            // Append -bullseye or -buster to pin to an OS version.
+            // Use -bullseye variants on local on arm64/Apple Silicon.
+            "VARIANT": "3.11",
+            // Options
+            "NODE_VERSION": "none"
+        }
+    },
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/usr/local/bin/python",
+                "python.linting.enabled": true,
+                "python.linting.pylintEnabled": true,
+                "python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
+                "python.formatting.blackPath": "/usr/local/py-utils/bin/black",
+                "python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
+                "python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
+                "python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
+                "python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
+                "python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
+                "python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
+                "python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
+            },
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": [
+                "ms-python.python",
+                "ms-python.vscode-pylance"
+            ]
+        }
+    },
+    // Use 'forwardPorts' to make a list of ports inside the container available locally.
+    // Use 'postCreateCommand' to run commands after the container is created.
+    // "postCreateCommand": "pip3 install --user -r requirements.txt",
+    // Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+    "remoteUser": "root"
+}

.github/CONTRIBUTING.rst

@@ -0,0 +1,35 @@
+Contributing to the project
+===========================
+
+Contributions and issues are most welcome! All issues and pull requests are
+handled through GitHub_. 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.
+
+.. _GitHub: https://github.com/DiamondLightSource/diffcalc-api/issues
+
+Issue or Discussion?
+--------------------
+
+Github also offers 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.
+
+.. _discussions: https://github.com/DiamondLightSource/diffcalc-api/discussions
+
+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 guide
+---------------
+
+The `Developer Guide`_ contains information on setting up a development
+environment, running the tests and what standards the code and documentation
+should follow.
+
+.. _Developer Guide: https://diamondlightsource.github.io/diffcalc-api/master/developer/how-to/contribute.html

.github/actions/install_requirements/action.yml

@@ -0,0 +1,58 @@
+name: Install requirements
+description: Run pip install with requirements and upload resulting requirements
+inputs:
+  requirements_file:
+    description: Name of requirements file to use and upload
+    required: true
+  install_options:
+    description: Parameters to pass to pip install
+    required: true
+  python_version:
+    description: Python version to install
+    default: "3.x"
+
+runs:
+  using: composite
+
+  steps:
+    - name: Setup python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ inputs.python_version }}
+
+    - name: Pip install
+      run: |
+        touch ${{ inputs.requirements_file }}
+        # -c uses requirements.txt as constraints, see 'Validate requirements file'
+        pip install -c ${{ inputs.requirements_file }} ${{ inputs.install_options }}
+      shell: bash
+
+    - name: Create lockfile
+      run: |
+        mkdir -p lockfiles
+        pip freeze --exclude-editable > lockfiles/${{ inputs.requirements_file }}
+        # delete the self referencing line and make sure it isn't blank
+        sed -i '/file:/d' lockfiles/${{ inputs.requirements_file }}
+      shell: bash
+
+    - name: Upload lockfiles
+      uses: actions/upload-artifact@v3
+      with:
+        name: lockfiles
+        path: lockfiles
+
+    # This eliminates the class of problems where the requirements being given no
+    # longer match what the packages themselves dictate. E.g. In the rare instance
+    # where I install some-package which used to depend on vulnerable-dependency
+    # but now uses good-dependency (despite being nominally the same version)
+    # pip will install both if given a requirements file with -r
+    - name: If requirements file exists, check it matches pip installed packages
+      run: |
+        if [ -s ${{ inputs.requirements_file }} ]; then
+          if ! diff -u ${{ inputs.requirements_file }} lockfiles/${{ inputs.requirements_file }}; then
+            echo "Error: ${{ inputs.requirements_file }} need the above changes to be exhaustive"
+            exit 1
+          fi
+        fi
+      shell: bash
+

.github/pages/make_switcher.py

@@ -0,0 +1,99 @@
+import json
+import logging
+from argparse import ArgumentParser
+from pathlib import Path
+from subprocess import CalledProcessError, check_output
+from typing import List, Optional
+
+
+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: Optional[str], remove: Optional[str]) -> 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)
+    if remove:
+        assert remove in builds, f"Build '{remove}' not in {sorted(builds)}"
+        builds.remove(remove)
+
+    # 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("/")
+    struct = [
+        dict(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)
+
+
+def main(args=None):
+    parser = ArgumentParser(
+        description="Make a versions.txt file from gh-pages directories"
+    )
+    parser.add_argument(
+        "--add",
+        help="Add this directory to the list of existing directories",
+    )
+    parser.add_argument(
+        "--remove",
+        help="Remove this directory from 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, args.remove)
+    write_json(args.output, args.repository, versions)
+
+
+if __name__ == "__main__":
+    main()