Hotfix/bug fixes

.github/dependabot.yml

@@ -11,7 +11,7 @@ updates:
       interval: "daily"
       time: "00:00"
     reviewers:
-      - "kzscisoft"
+      - "ryanjfield"
     commit-message:
       prefix: "pip"
       include: "scope"

.github/workflows/deploy.yaml

@@ -6,7 +6,7 @@ on:
 permissions:
   contents: write
 jobs:
-  windows-py39:
+  windows-py3x:
     name: Deploy Latest Windows Release
     runs-on: windows-latest
     steps:
@@ -16,7 +16,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.9.7'
+          python-version: '3.x'
           architecture: "x64"
 
       - name: Get Previous tag
@@ -42,7 +42,7 @@ jobs:
             name: windows_faircli
             path: dist/fair-cli-${{ steps.previoustag.outputs.tag }}-x64-windows-latest.exe
 
-  macos-py39:
+  macos-py3x:
     name: Deploy Latest macOS Release
     runs-on: macos-latest
     steps:
@@ -52,7 +52,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.9.7'
+          python-version: '3.x'
           architecture: "x64"
 
       - name: Install Poetry
@@ -79,7 +79,7 @@ jobs:
             path: dist/fair-cli-${{ steps.previoustag.outputs.tag }}-x64-macos-latest
 
 
-  ubuntu-py39:
+  ubuntu-py3x:
     name: Deploy Latest Linux Release
     runs-on: ubuntu-latest
     steps:
@@ -89,7 +89,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.9.7'
+          python-version: '3.x'
           architecture: "x64"
 
       - name: Install Poetry
@@ -120,16 +120,16 @@ jobs:
     name: Create Release
     runs-on: ubuntu-latest
     needs:
-      - ubuntu-py39
-      - macos-py39
-      - windows-py39
+      - ubuntu-py3x
+      - macos-py3x
+      - windows-py3x
     steps:
       - uses: actions/checkout@v3
         with:
             fetch-depth: 0
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.9.7'
+          python-version: '3.x'
           architecture: "x64"
 
       - name: Install Poetry

.github/workflows/fair-cli.yaml

@@ -7,31 +7,50 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest] #, macos-latest, windows-latest]
-        # Issues with GitPython and Python >3.9.6, <3.10
+        os: [ubuntu-latest, macos-latest, windows-latest]
         python: ["3.8", "3.9", "3.10", "3.x"]
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v3
+        if: ${{ runner.os != 'Windows' }}
+      - name: Checkout to C windows
+        run: |
+          mkdir C:/FAIR-CLI
+          git clone https://github.com/FAIRDataPipeline/FAIR-CLI.git C:/FAIR-CLI
+          cd C:/FAIR-CLI
+          git checkout $GITHUB_REF_NAME
+          echo Github Ref: $GITHUB_REF_NAME
+        if: ${{ runner.os == 'Windows' }}
+        shell: bash
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
           architecture: "x64"
-      - name: Install Required
-        run: sudo apt install libmemcached-dev
-        if: matrix.os == 'ubuntu-latest'
-      - name: Install Required
-        run: brew install memcached
-        if: matrix.os == 'macos-latest'
       - name: Install Poetry
         run: python -m pip install poetry
       - name: Install Module
-        run: python -m poetry install
+        run: |
+          if [ "$RUNNER_OS" == "Windows" ]; then
+              cd C:/FAIR-CLI
+              pwd
+          fi
+          python -m poetry install
+        shell: bash
       - name: Install Python API for API Tests
-        run: python -m poetry run pip install git+https://github.com/FAIRDataPipeline/pyDataPipeline.git@dev
+        run: |
+          if [ "$RUNNER_OS" == "Windows" ]; then
+              cd C:/FAIR-CLI
+              pwd
+          fi
+          python -m poetry run pip install git+https://github.com/FAIRDataPipeline/pyDataPipeline.git@main
+        shell: bash
       - name: Run Tests for Each Marker
         run: |
+            if [ "$RUNNER_OS" == "Windows" ]; then
+              cd C:/FAIR-CLI
+              pwd
+            fi
             for marker in $(poetry run pytest --markers | grep -oE "faircli_[a-zA-Z|_|0-9]+")
             do
               echo "Running tests for marker '$marker'"
@@ -41,6 +60,7 @@ jobs:
                 echo "ERROR: Tests for marker '$marker' failed"
               fi
             done
+        shell: bash
       - uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/implementations.yml

@@ -50,6 +50,8 @@ jobs:
           ${GITHUB_WORKSPACE}/registry-rem/scripts/start_fair_registry -p 8001 -s drams.test-remote-settings
           # Copy the remote token
           cp ${GITHUB_WORKSPACE}/registry-rem/token $PWD/token
+          export DJANGO_SETTINGS_MODULE=drams.test-remote-settings
+          ${GITHUB_WORKSPACE}/registry-rem/venv/bin/python  ${GITHUB_WORKSPACE}/registry-rem/manage.py createsuperuser --username FAIRDataPipeline --noinput
         working-directory: pySimpleModel
 
       - name: Install the registry and init

.gitignore

@@ -148,6 +148,7 @@ cython_debug/
 
 # Misc
 *.yaml
+!tests/data/*.yaml
 *.yml
 token.txt
 .fair

CITATION.cff

@@ -36,4 +36,4 @@ license: BSD-2-Clause
 message: If you use this software, please cite it using these metadata.
 repository-code: https://github.com/FAIRDataPipeline/FAIR-CLI/
 title: "The FAIR Data Pipeline command line tool"
-version: 0.7.3
+version: 0.8.0

fair/cli.py

@@ -105,8 +105,7 @@ def status(verbose, debug) -> None:
     except fdp_exc.FAIRCLIException as e:
         e.err_print()
         if e.level.lower() == "error":
-            if e.level.lower() == "error":
-                sys.exit(e.exit_code)
+            sys.exit(e.exit_code)
 
 @cli.group(invoke_without_command=True)
 @click.option("--debug/--no-debug", help="Run in debug mode", default=False)
@@ -118,8 +117,10 @@ def list(ctx, debug, remote) -> None:
         ctx.obj = {}
     ctx.obj['DEBUG'] = debug
     ctx.obj['REMOTE'] = remote
-    ctx.invoke(data_products)
-    ctx.invoke(code_runs)
+    _current_args = " ".join(sys.argv)
+    if not ("data-products" in _current_args or "code-runs" in _current_args):
+        ctx.invoke(data_products)
+        ctx.invoke(code_runs)
 
 @list.command()
 @click.pass_context
@@ -161,7 +162,7 @@ def create(debug, output: str) -> None:
         if output
         else os.path.join(os.getcwd(), fdp_com.USER_CONFIG_FILE)
     )
-    click.echo(f"Generating new user configuration file" f" '{output}'")
+    click.echo(f"Generating new user configuration file '{output}'")
     with fdp_session.FAIR(os.getcwd(), debug=debug) as fair_session:
         fair_session.make_starter_config(output)
 
@@ -527,6 +528,7 @@ def run(
 ):
     """Initialises a job with the option to specify a bash command"""
     # Allow no config to be specified, if that is the case use default local
+    click.echo("Running run please wait")
     config = config[0] if config else fdp_com.local_user_config(os.getcwd())
     try:
         with fdp_session.FAIR(
@@ -636,6 +638,7 @@ def modify(ctx, label: str, url: str, debug: bool) -> None:
 )
 def push(remote: str, debug: bool, dirty: bool):
     """Push data between the local and remote registry"""
+    click.echo("Running push please wait")
     remote = remote[0] if remote else "origin"
     try:
         with fdp_session.FAIR(
@@ -679,6 +682,7 @@ def config_email(user_email: str) -> None:
 )
 def pull(config: str, debug: bool, local: bool):
     """Update local registry from remotes and sources"""
+    click.echo("Running pull please wait")
     config = config[0] if config else fdp_com.local_user_config(os.getcwd())
     try:
         with fdp_session.FAIR(

fair/common.py

@@ -296,4 +296,11 @@ def set_file_permissions(path: str):
         for dir in [os.path.join(root,d) for d in dirs]:
             os.chmod(dir, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO)
         for file in [os.path.join(root, f) for f in files]:
-            os.chmod(file, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO)
+            os.chmod(file, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO)
+
+def remove_readonly(fn, path, excinfo):
+    try:
+        os.chmod(path, stat.S_IWRITE)
+        fn(path)
+    except Exception as exc:
+        print("Skipped:", path, "because:\n", exc)