WIP: New queue

.copier-answers.yml

@@ -15,4 +15,3 @@ repository_namespace: Matgenix
 repository_provider: https://github.com/
 short_description: jobflow-remote is a python package to run jobflow workflows on
     remote resources
-

.github/workflows/testing.yml

@@ -2,9 +2,16 @@ name: testing
 
 on:
   push:
+    branches:
+    - develop
 
   pull_request:
-    branches: [main]
+
+# Cancel running workflows when additional changes are pushed
+# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#example-using-a-fallback-value
+concurrency:
+  group: ${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
 
 jobs:
   lint:
@@ -14,7 +21,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.9'
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -29,8 +36,9 @@ jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
 
     steps:
       - uses: actions/checkout@v3
@@ -48,23 +56,3 @@ jobs:
 
       - name: Test
         run: pytest --cov=jobflow_remote --cov-report=xml
-
-  docs:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.11'
-          cache: pip
-          cache-dependency-path: pyproject.toml
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[strict,docs]
-
-      - name: Build
-        run: jupyter-book build docs --path-output docs_build

.gitignore

@@ -154,3 +154,6 @@ cython_debug/
 
 # PyCharm
 .idea/
+
+# macOS
+.DS_store

.pre-commit-config.yaml

@@ -1,25 +1,25 @@
 default_language_version:
-  python: python3
+  python: python3.9
 #exclude: '^src/{{ package_name }}/some/directory/'
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/myint/autoflake
-  rev: v2.0.0
+  rev: v2.2.1
   hooks:
   - id: autoflake
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 23.9.1
   hooks:
   - id: black
 - repo: https://github.com/asottile/blacken-docs
-  rev: v1.12.1
+  rev: 1.16.0
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -29,18 +29,18 @@ repos:
   hooks:
   - id: isort
 - repo: https://github.com/pycqa/flake8
-  rev: 6.0.0
+  rev: 6.1.0
   hooks:
   - id: flake8
     entry: pflake8
     files: ^src/
     additional_dependencies:
-    - pyproject-flake8==6.0.0
-    - flake8-bugbear==22.12.6
-    - flake8-typing-imports==1.14.0
-    - flake8-docstrings==1.6.0
-    - flake8-rst-docstrings==0.3.0
-    - flake8-rst==0.8.0
+    - pyproject-flake8
+    - flake8-bugbear
+    - flake8-typing-imports
+    - flake8-docstrings
+    - flake8-rst-docstrings
+    - flake8-rst
 - repo: https://github.com/pre-commit/pygrep-hooks
   rev: v1.10.0
   hooks:
@@ -49,7 +49,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.991
+  rev: v1.6.0
   hooks:
   - id: mypy
     files: ^src/
@@ -58,13 +58,13 @@ repos:
     - types-pkg_resources==0.1.2
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.2
+  rev: v2.2.6
   hooks:
   - id: codespell
     stages: [commit, commit-msg]
-    args: [--ignore-words-list, 'titel,statics,ba,nd,te']
+    args: [--ignore-words-list, 'titel,statics,ba,nd,te,nin']
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.3.1
+  rev: v3.15.0
   hooks:
     - id: pyupgrade
       args: [--py38-plus]

README.md

@@ -7,11 +7,7 @@
 
 **[Full Documentation][docs]**
 
-jobflow-remote is a Python software for ... Features of jobflow-remote include
-
-- Feature A
-- Feature B
-- ...
+jobflow-remote is a Python package to run jobflow workflows on remote resources.
 
 ## Quick start
 
@@ -60,12 +56,12 @@ jobflow-remote is developed and maintained by Matgenix SRL.
 
 A full list of all contributors can be found [here][contributors].
 
-[help-forum]: https://https://github.com//Matgenix/jobflow_remote/issues
-[issues]: https://https://github.com//Matgenix/jobflow_remote/issues
-[installation]: https://https://github.com//Matgenix/jobflow_remote/blob/main/INSTALL.md
-[contributing]: https://github.com/Matgenix/jobflow_remote/blob/main/CONTRIBUTING.md
-[codeofconduct]: https://github.com/Matgenix/jobflow_remote/blob/main/CODE_OF_CONDUCT.md
-[changelog]: https://https://github.com//Matgenix/jobflow_remote/blob/main/CHANGELOG.md
-[contributors]: https://Matgenix.github.io/jobflow_remote/graphs/contributors
-[license]: https://raw.githubusercontent.com/Matgenix/jobflow_remote/main/LICENSE
-[docs]: https://Matgenix.github.io/jobflow_remote/
+[help-forum]: https://github.com//Matgenix/jobflow-remote/issues
+[issues]: https://github.com//Matgenix/jobflow-remote/issues
+[installation]: https://https://github.com//Matgenix/jobflow-remote/blob/main/INSTALL.md
+[contributing]: https://github.com/Matgenix/jobflow-remote/blob/main/CONTRIBUTING.md
+[codeofconduct]: https://github.com/Matgenix/jobflow-remote/blob/main/CODE_OF_CONDUCT.md
+[changelog]: https://github.com//Matgenix/jobflow-remote/blob/main/CHANGELOG.md
+[contributors]: https://Matgenix.github.io/jobflow-remote/graphs/contributors
+[license]: https://raw.githubusercontent.com/Matgenix/jobflow-remote/blob/main/LICENSE
+[docs]: https://Matgenix.github.io/jobflow-remote/

doc/Makefile

@@ -0,0 +1,72 @@
+# Makefile for Sphinx documentation
+#
+
+# PYVER needs to be major.minor, just "3" doesn't work - it will result in
+# issues with the amendments to PYTHONPATH and install paths (see DIST_VARS).
+
+# Use explicit "version_info" indexing since make cannot handle colon characters, and
+# evaluate it now to allow easier debugging when printing the variable
+
+PYVER:=$(shell python3 -c 'from sys import version_info as v; print("{0}.{1}".format(v[0], v[1]))')
+PYTHON = python$(PYVER)
+
+# You can set these variables from the command line.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= LANG=C sphinx-build
+PAPER         ?=
+# # For merging a documentation archive into a git checkout of numpy/doc
+# # Turn a tag like v1.18.0 into 1.18
+# # Use sed -n -e 's/patttern/match/p' to return a blank value if no match
+# TAG ?= $(shell git describe --tag | sed -n -e's,v\([1-9]\.[0-9]*\)\.[0-9].*,\1,p')
+
+FILES=
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -WT --keep-going -d build/doctrees $(PAPEROPT_$(PAPER)) \
+                  $(SPHINXOPTS) source
+
+.PHONY: help clean html version-check html-build
+
+#------------------------------------------------------------------------------
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  clean     to remove generated doc files and start fresh"
+	@echo "  html      to make standalone HTML files"
+
+clean:
+	-rm -rf build/*
+	find . -name generated -type d -prune -exec rm -rf "{}" ";"
+
+
+#------------------------------------------------------------------------------
+# Automated generation of all documents
+#------------------------------------------------------------------------------
+
+# Build the current QToolKit version, and extract docs from it.
+# We have to be careful of some issues:
+#
+# - Everything must be done using the same Python version
+#
+
+#SPHINXBUILD="LANG=C sphinx-build"
+
+
+#------------------------------------------------------------------------------
+# Basic Sphinx generation rules for different formats
+#------------------------------------------------------------------------------
+generate: build/generate-stamp
+build/generate-stamp: $(wildcard source/reference/*.rst)
+	mkdir -p build
+	touch build/generate-stamp
+
+html: api-doc html-build
+html-build: generate
+	mkdir -p build/html build/doctrees
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) build/html $(FILES)
+	@echo
+	@echo "Build finished. The HTML pages are in build/html."
+api-doc:
+	sphinx-apidoc -e -f -o source/api ../src/jobflow_remote

doc/source/_static/index-images/image_licences.txt

@@ -0,0 +1,4 @@
+getting_started.svg: https://www.svgrepo.com/svg/393367/rocket (PD Licence)
+user_guide.svg: https://www.svgrepo.com/svg/75531/user-guide (CC0 Licence)
+api.svg: https://www.svgrepo.com/svg/157898/gears-configuration-tool (CC0 Licence)
+contributor.svg: https://www.svgrepo.com/svg/57189/code-programing-symbol (CC0 Licence)