merge with main

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 120
+ignore = N812,W605,F401,E127

.github/workflows/ci.yaml

@@ -0,0 +1,50 @@
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  direct:
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      matrix:
+        # apsw not available for macos
+        os: [ubuntu]  # , macos]
+        # apsw not available for 3.10, not installable via tar
+        python-version: ['3.6', '3.7', '3.8', '3.9']  # , '3.10']
+        poetry-version: [1.1.11]
+
+    steps:
+      - name: Checkout cgat-daisy
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Run image
+        uses: abatilo/[email protected]
+        with:
+          poetry-version: ${{ matrix.poetry-version }}
+
+      - name: Poetry install
+        run: poetry install
+
+      - name: Poetry install
+        run: poetry run pytest
+
+      # - name: Install prerequisite Python libraries
+      #   run: |
+      #     python -m pip install --upgrade pip
+      #     pip install pytest pytest-pep8 flake8
+      #     if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      # - name: Lint with flake8
+      #   run: |
+      #     # stop the build if there are Python syntax errors or undefined names
+      #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+      #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+      #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      # - name: Test with pytest
+      #   run: |
+      #     pytest

.github/workflows/release.yaml

@@ -0,0 +1,69 @@
+name: Publish cgat-daisy wheels to PyPI and TestPyPI
+
+on:
+  push:
+    branches:
+      - v[0-9]+.[0-9]+*
+    tags:
+      - v*
+  release:
+    types:
+      - published
+
+jobs:
+  build:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+
+    steps:
+      - name: Checkout cgat-daisy
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+
+      - name: Run image
+        uses: abatilo/[email protected]
+
+      - name: Poetry install
+        run: poetry build --format=sdist
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v2
+        with:
+          path: dist/*
+
+  upload_pypi:
+
+    needs: [build]
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Get Artifacts
+        uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+
+      - name: Publish distribution to Test PyPI
+        if: github.event_name == 'push'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          verbose: true
+          user: __token__
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+          repository_url: https://test.pypi.org/legacy/
+
+      - name: Publish distribution to PyPI
+        if: github.event_name == 'release' && github.event.action == 'published'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          verbose: true
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+

README.md

@@ -0,0 +1,33 @@
+# Daisy/CGAT Bench
+
+Daisy is a system to design and execute benchmarking tasks.
+
+After installation, use the ``daisy`` command to see how to use them.
+
+For questions, please open a discussion on the GitHub 
+`issue page <https://github.com/cgat-developers/cgat-daisy/issues>`_.
+
+Installation
+============
+
+daisy is available via pypi:
+
+```
+pip install cgat-daisy
+```
+
+or in conda:
+
+```
+conda install cgat-daisy
+```
+
+Usage
+=====
+
+Run the ``daisy --help`` for the tools that are available.
+
+Documentation
+=============
+
+Full documentation is on RTD (WIP)

doc/collect.py

@@ -46,7 +46,7 @@ def main(argv=None):
         tool_module = re.sub(".py", "", os.path.basename(tool))
         tool_name = re.sub("_", "-", tool_module)
         if tool_name in ("__init__", "cli"):
-            c.ignored += 1
+            counter.ignored += 1
             continue
 
         dest = os.path.join("tools", "{}.rst".format(tool_name))