Merge pull request #1 from Alafia-Ai/20220414-fs-source

Brings 20220414-fs-source branch up to date with ReproNim/master

.autorc

@@ -0,0 +1,7 @@
+{
+    "onlyPublishWithReleaseLabel": true,
+    "baseBranch": "master",
+    "author": "Repronim Bot <[email protected]>",
+    "noVersionPrefix": true,
+    "plugins": ["git-tag"]
+}

.codespellrc

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+[codespell]
+skip = .git,*.pdf,*.svg,versioneer.py,_version.py
+# didi -- some name Dear to someone
+ignore-words-list = didi

.dockerignore

@@ -1,7 +1,3 @@
-# Sphinx documentation.
-# The Docker image is not intended to be used to build docs.
-/docs
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.et

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+{ "bad_versions" : ["0.9.2", "0.9.3"]
+}

.github/dependabot.yml

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+---
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+-   package-ecosystem: github-actions
+    directory: /
+    schedule:
+        interval: weekly

.github/workflows/bootstrap.yml

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+# this workflow bootstraps the testing of the build the docker images
+#
+# - this will run the python script used to generate the workflows
+#   based on a the jinja template
+# - commit and push the generated workflows to the branch test_docker_build
+#   where they will be executed
+
+name: bootstrap
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  push:
+    branches: [ "master" ]
+    paths:
+      - .github/workflows/bootstrap.yml
+      - .github/workflows/create_workflows.py
+      - neurodocker/**
+
+# Uses the cron schedule for github actions
+#
+# https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#scheduled-events
+#
+#         ┌───────────── minute (0 - 59)
+#         │ ┌───────────── hour (0 - 23)
+#         │ │   ┌───────────── day of the month (1 - 31)
+#         │ │   │    ┌───────────── month (1 - 12 or JAN-DEC)
+#         │ │   │    │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+#         │ │   │    │ │
+#         │ │   │    │ │
+#         │ │   │    │ │
+#         * *   *    * *
+
+  schedule:
+  - cron: 0 0 1,15 * *
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    inputs:
+      software_name:
+        description: 'software to test'
+        required: true
+        default: 'all'
+
+permissions:
+  contents: write
+  actions: write
+jobs:
+  bootstrap:
+    runs-on: ubuntu-22.04
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.CI_FLOW }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: python -m pip install jinja2 pyyaml
+
+      - name: Create workflows
+        run: |
+          software_name=${{ inputs.software_name }}
+          if [ -z "$software_name" ]; then
+            software_name="all"
+          fi
+          if [ "$software_name" = "all" ]; then
+            echo "testing all software"
+          else
+            echo "testing ${software_name}"
+          fi
+          git checkout -b test_docker_build
+          python .github/workflows/create_workflows.py --software_name ${software_name}
+          ls -l .github/workflows
+          git add .
+          git config --global user.email "[email protected]"
+          git config --global user.name "Repronim neurodocker bot"
+          git commit -am "added new workflows"
+          git push origin --force test_docker_build

.github/workflows/codespell.yml

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+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/create_workflows.py

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+"""
+This scripts uses a jinja template to create CI workflows to test.
+
+    - different linux distributions (split by the package manager they use)
+    - different software that neurodocker supports
+    - different install method for a given software
+
+All of those are defined in a python dictionary.
+
+Versions to install are read from the neurodocker template for a given software.
+It is possible to skip a version by adding a "skip_versions" key to the software.
+
+Each workflow:
+
+    - installs the latest version of neurodocker
+    - builds a dockerfile for a combination of OS / software / version / install method
+    - cat the dockerfile
+    - attempts to build the corresponding image
+
+This script will also create a "dashboard" saved in docs/README.md
+to be picked up to be rendered by the github pages.
+This requires for you to build the pages from the docs folder
+and on the branch where the workflows are pushed to (currently "test_docker_build").
+
+"""
+import argparse
+from pathlib import Path
+
+import yaml  # type: ignore
+from jinja2 import Environment, FileSystemLoader, select_autoescape
+
+apt_based = [
+    "ubuntu:22.04",
+    "ubuntu:18.04",
+    "debian:bullseye-slim",
+    "debian:buster-slim",
+]
+yum_based = ["fedora:36", "centos:7"]
+
+"""
+Add a "skip_versions" key to the software dictionary if you want to skip
+testing a specific version. For example, if you want to skip testing
+version 1.0.0 of afni, add the following to the software dictionary:
+
+    "afni": {
+            "skip_versions": ["1.0.0"],
+            "methods": ["binaries", "source"],
+            "afni_python": ["true", "false"],
+        },
+
+"""
+output_dir = Path(__file__).parent
+
+template_folder = Path(__file__).parents[2].joinpath("neurodocker", "templates")
+
+build_dashboard_file = Path(__file__).parents[2].joinpath("docs", "README.md")
+
+# this has to match the name of the branch where the workflows are pushed to
+# see .github/workflows/bootstrap.yml
+branch = "test_docker_build"
+
+# Update to match your username and repo name if you are testing things on your fork
+# "ReproNim/neurodocker"
+repo = "ReproNim/neurodocker"
+
+
+def software() -> dict[str, dict[str, list[str]]]:
+    return {
+        "afni": {
+            "methods": ["binaries", "source"],
+            "afni_python": ["true", "false"],
+        },
+        "ants": {
+            "methods": ["binaries", "source"],
+        },
+        "cat12": {"methods": ["binaries"]},
+        "convert3d": {"methods": ["binaries"]},
+        "dcm2niix": {
+            "methods": ["binaries", "source"],
+        },
+        "freesurfer": {"methods": []},
+        "fsl": {
+            "methods": ["binaries"],
+        },
+        "matlabmcr": {
+            "methods": ["binaries"],
+        },
+        "mricron": {"methods": ["binaries"]},
+        "mrtrix3": {
+            "methods": ["binaries", "source"],
+        },
+        "spm12": {"methods": ["binaries"]},
+        "miniconda": {},
+    }
+
+
+def create_dashboard_file():
+    """Create a build dashboard file."""
+
+    print("creating build dashboard file...")
+    print(build_dashboard_file)
+
+    gh_actions_url = "http://github-actions.40ants.com/"
+
+    with open(build_dashboard_file, "w") as f:
+        image_base_url = f"{gh_actions_url}{repo}/matrix.svg?branch={branch}"
+        print(
+            """<!-- This page is generated automatically. Do not edit manually. -->
+# Build dashboard
+""",
+            file=f,
+        )
+
+        # table of content
+        for software_, _ in software().items():
+            print(f"""- [{software_}](#{software_})""", file=f)
+
+        print("", file=f)
+
+        # link to the github actions workflow and image of the build status
+        for software_, _ in software().items():
+            image_url = f"{image_base_url}&only={software_}"
+            print(
+                f"""## {software_}
+
+[{software_} workflow](https://github.com/{repo}/actions/workflows/{software_}.yml)
+
+![{software_} build status]({image_url})
+""",
+                file=f,
+            )
+
+
+def get_versions_from_neurodocker_template(software: str) -> list[str]:
+    """Load the list of versions to test from the software template."""
+    template = template_folder.joinpath(software).with_suffix(".yaml")
+    with open(template, "r") as f:
+        data = yaml.load(f, Loader=yaml.FullLoader)
+    return list(data["binaries"]["urls"].keys())
+
+
+def stringify(some_list: list[str]) -> str:
+    if len(some_list) == 1:
+        return f"'{some_list[0]}'"
+    return "'" + "', '".join(some_list) + "'"
+
+
+def main(software_name="all"):
+    env = Environment(
+        loader=FileSystemLoader(Path(__file__).parent),
+        autoescape=select_autoescape(),
+        lstrip_blocks=True,
+        trim_blocks=True,
+    )
+
+    template = env.get_template("docker_build.jinja")
+
+    os = {
+        "apt_based": stringify(apt_based),
+        "yum_based": stringify(yum_based),
+        "all": stringify(apt_based + yum_based),
+    }
+
+    # only keep relevant software
+    software_to_test = software()
+    if software_name in software_to_test:
+        software_to_test = {software_name: software_to_test[software_name]}
+
+    for software_, spec in software_to_test.items():
+        wf = {
+            "header": "# This is file is automatically generated. Do not edit.",
+            "os": os,
+            "software": software_,
+        }
+
+        versions = get_versions_from_neurodocker_template(software_)
+        for i in spec.get("skip_versions", []):
+            versions.remove(i)
+        if software_ == "miniconda":
+            versions = ["latest"]
+
+        if versions is not None and len(versions) > 0:
+            wf["add_version"] = True
+            wf["versions"] = stringify(versions)
+
+        if spec.get("methods") is not None and len(spec["methods"]) > 0:
+            wf["add_method"] = True
+            wf["methods"] = stringify(spec["methods"])
+
+        if spec.get("afni_python") is not None and len(spec["afni_python"]) > 0:
+            wf["add_afni_python"] = True
+            wf["afni_python"] = stringify(spec["afni_python"])
+
+        output_file = output_dir.joinpath(software_).with_suffix(".yml")
+        print("creating workflow")
+        print(f"{output_file}")
+        with open(output_file, "w") as f:
+            print(template.render(wf=wf), file=f)
+
+    create_dashboard_file()
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+
+    choices = list(software().keys())
+    choices.append("all")
+
+    parser.add_argument(
+        "--software_name",
+        required=False,
+        default="all",
+        choices=choices,
+        nargs=1,
+    )
+    args = parser.parse_args()
+
+    main(software_name=args.software_name[0])