initial commit

.github/workflows/tag_and_publish.yml

@@ -3,87 +3,77 @@ on:
   push:
     branches:
       - main
-# Remove line 61 to enable automated semantic version bumps.
-# Change line 67 from "if: false" to "if: true" to enable PyPI publishing. 
-# Requires that svc-aindscicomp be added as an admin to repo.
 jobs:
-  update_badges:
+  tag:
+    name: Bump version
     runs-on: ubuntu-latest
-    continue-on-error: true
+    outputs:
+      new_version: ${{ steps.output_version.outputs.new_version }}
     steps:
-    - uses: actions/checkout@v3
+    - name: Checkout
+      uses: actions/checkout@v3
       with:
-        ref: ${{ env.DEFAULT_BRANCH }}
+        ref: "main"
         fetch-depth: 0
         token: ${{ secrets.SERVICE_TOKEN }}
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.8
-    - name: Install dependencies
-      run: | 
-        python -m pip install -e .[dev] --no-cache-dir
-    - name: Get Python version and Update README.md
-      run: |
-        python_version=$(grep "requires-python" pyproject.toml | grep -o ">=[^\"]*")
-        python_badge=$(grep -o 'python-[^)]*' README.md)
-        new_python_badge="python-$python_version-blue?logo=python"
-        sed -i "s/$python_badge/$new_python_badge/g" README.md
-    - name: Get interrogate values and Update README.md
-      run: |
-        interrogate_val=$(interrogate . | grep -o 'actual: [0-9]*\.[0-9]*' | awk '{print $2}')
-        interrogate_badge=$(grep -o 'interrogate-[^)]*' README.md)
-        if (( $(echo "$interrogate_val >= 90.00" | bc -l) )); then
-            new_interrogate_badge="interrogate-$interrogate_val%25-brightgreen"
-        elif (( $(echo "$interrogate_val < 80.00" | bc -l) )); then
-            new_interrogate_badge="interrogate-$interrogate_val%25-red"
-        else
-            new_interrogate_badge="interrogate-$interrogate_val%25-yellow"
-        fi
-        sed -i "s/$interrogate_badge/$new_interrogate_badge/g" README.md
-    - name: Get Coverage values and Update README.md
-      run: |
-        coverage run -m unittest discover
-        coverage_val=$(coverage report | grep "^TOTAL" | grep -o '[0-9]\+%' | grep -o '[0-9]\+')
-        coverage_badge=$(grep -o "coverage-[^?]*" README.md)
-        if (( $(echo "$coverage_val >= 90.00" | bc -l) )); then 
-            new_coverage_badge="coverage-$coverage_val%25-brightgreen"
-        elif (( $(echo "$coverage_val < 80.00" | bc -l) )); then
-            new_coverage_badge="coverage-$coverage_val%25-red"
-        else
-            new_coverage_badge="coverage-$coverage_val%25-yellow"
-        fi
-        sed -i "s/$coverage_badge/$new_coverage_badge/g" README.md
-    - name: Commit changes
-      uses: EndBug/add-and-commit@v9
+    - name: Compute new version number
+      id: tag_version
+      uses: mathieudutour/[email protected]
       with:
-        default_author: github_actions
-        message: "ci: update badges [skip actions]"
-        add: '["README.md"]'
-  tag:
-    needs: update_badges
-    if: ${{github.event.repository.name == 'aind-library-template'}}
-    uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main
-    secrets:
-      SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }}
+        github_token: ${{ secrets.SERVICE_TOKEN }}
+        release_branches: "main"
+        default_bump: patch
+        dry_run: false
   publish:
-    needs: tag
-    if: false
     runs-on: ubuntu-latest
+    env:
+      GO_VERSION: '1.14.12'
+      GO_OS: 'linux'
+      GO_ARCH: 'amd64'
+      SINGULARITY_VERSION: '3.7.0'
+    needs: tag
     steps:
       - uses: actions/checkout@v3
       - name: Pull latest changes
         run: git pull origin main
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
       - name: Install dependencies
         run: |
-          pip install --upgrade setuptools wheel twine build
-          python -m build
-          twine check dist/*
-      - name: Publish on PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.AIND_PYPI_TOKEN }}
+          sudo apt-get update && sudo apt-get install -y \
+          build-essential \
+          libssl-dev \
+          uuid-dev \
+          libgpgme11-dev \
+          squashfs-tools \
+          libseccomp-dev \
+          wget \
+          pkg-config \
+          procps
+      - name: Install GO
+        run: |
+          wget https://dl.google.com/go/go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz
+          sudo tar -C /usr/local -xzvf go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz
+          sudo rm go$GO_VERSION.$GO_OS-$GO_ARCH.tar.gz
+          echo 'export PATH=$PATH:/usr/local/go/bin' | sudo tee -a /etc/profile
+      - name: Install Singularity
+        run: |
+          cd ..
+          wget https://github.com/hpcng/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz
+          sudo tar -xzf singularity-${SINGULARITY_VERSION}.tar.gz
+          sudo rm singularity-${SINGULARITY_VERSION}.tar.gz
+          echo "Finished installing binaries"
+          export PATH=$PATH:/usr/local/go/bin
+          cd singularity
+          sudo ./mconfig --without-suid
+          sudo make -C ./builddir
+          sudo make -C ./builddir install
+      - name: Build sif container
+        run: |
+          ls /
+          ls
+          mkdir build
+          sudo singularity build build/container.sif scripts/singularity_build.def
+      - name: Login and Deploy Container
+        run: |
+          echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io
+          singularity push build/container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${{ needs.tag.outputs.new_version }}
+          singularity push build/container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:latest

README.md

@@ -1,100 +1,9 @@
 # aind-data-upload
 
+Repository to manage uploading data to the cloud
+
 [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
-![Code Style](https://img.shields.io/badge/code%20style-black-black)
 [![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
-![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen)
-![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
-![Python](https://img.shields.io/badge/python->=3.7-blue?logo=python)
-
-
 
 ## Usage
- - To use this template, click the green `Use this template` button and `Create new repository`.
- - After github initially creates the new repository, please wait an extra minute for the initialization scripts to finish organizing the repo.
- - To enable the automatic semantic version increments: in the repository go to `Settings` and `Collaborators and teams`. Click the green `Add people` button. Add `svc-aindscicomp` as an admin. Modify the file in `.github/workflows/tag_and_publish.yml` and remove the if statement in line 10. The semantic version will now be incremented every time a code is committed into the main branch.
- - To publish to PyPI, enable semantic versioning and uncomment the publish block in `.github/workflows/tag_and_publish.yml`. The code will now be published to PyPI every time the code is committed into the main branch.
- - The `.github/workflows/test_and_lint.yml` file will run automated tests and style checks every time a Pull Request is opened. If the checks are undesired, the `test_and_lint.yml` can be deleted. The strictness of the code coverage level, etc., can be modified by altering the configurations in the `pyproject.toml` file and the `.flake8` file.
-
-## Installation
-To use the software, in the root directory, run
-```bash
-pip install -e .
-```
-
-To develop the code, run
-```bash
-pip install -e .[dev]
-```
-
-## Contributing
-
-### Linters and testing
-
-There are several libraries used to run linters, check documentation, and run tests.
-
-- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
-
-```bash
-coverage run -m unittest discover && coverage report
-```
-
-- Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
-
-```bash
-interrogate .
-```
-
-- Use **flake8** to check that code is up to standards (no unused imports, etc.):
-```bash
-flake8 .
-```
-
-- Use **black** to automatically format the code into PEP standards:
-```bash
-black .
-```
-
-- Use **isort** to automatically sort import statements:
-```bash
-isort .
-```
-
-### Pull requests
-
-For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use [Angular](https://github.com/angular/angular/blob/main/CONTRIBUTING.md#commit) style for commit messages. Roughly, they should follow the pattern:
-```text
-<type>(<scope>): <short summary>
-```
-
-where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:
-
-- **build**: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
-- **ci**: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
-- **docs**: Documentation only changes
-- **feat**: A new feature
-- **fix**: A bugfix
-- **perf**: A code change that improves performance
-- **refactor**: A code change that neither fixes a bug nor adds a feature
-- **test**: Adding missing tests or correcting existing tests
-
-### Semantic Release
-
-The table below, from [semantic release](https://github.com/semantic-release/semantic-release), shows which commit message gets you which release type when `semantic-release` runs (using the default configuration):
-
-| Commit message                                                                                                                                                                                   | Release type                                                                                                    |
-| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------- |
-| `fix(pencil): stop graphite breaking when too much pressure applied`                                                                                                                             | ~~Patch~~ Fix Release, Default release                                                                          |
-| `feat(pencil): add 'graphiteWidth' option`                                                                                                                                                       | ~~Minor~~ Feature Release                                                                                       |
-| `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit) |
-
-### Documentation
-To generate the rst files source files for documentation, run
-```bash
-sphinx-apidoc -o doc_template/source/ src 
-```
-Then to create the documentation HTML files, run
-```bash
-sphinx-build -b html doc_template/source/ doc_template/build/html
-```
-More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
+We can add additional python if needed. For now, this will publish a singularity container with `awscli` installed. Most jobs will just use the sync command.