Merge branch 'QCoDeS:master' into master

Author: thangleiter

.github/ISSUE_TEMPLATE.md

@@ -1,19 +1,32 @@
-If you encounter a bug use the following template.
-If you have a feature request feel free to freestyle.
+If you encounter a bug, use the following template.
+If you have a feature request feel free to freestyle or use ideas section in the discussions
+[here](https://github.com/QCoDeS/Qcodes/discussions).
+If you have a question or general opinion, open your query on a relevant discussion section.
+
+Bug report template:
+
+###
+A good title and description
+
 ### Steps to reproduce
 1.
 2.
 3.
 
 ### Expected behaviour
-Tell us what should happen
+What did you expect to happen?
 
 ### Actual behaviour
-Tell us what happens instead
+What did happen instead?
 
 ### System
+It would be helpful to provide such information:
+
 **operating system**
 
-**qcodes branch**
+If you are using a released version of qcodes (recommended):
+**qcodes version**
 
+If you are using the development version of qcodes:
+**qcodes branch**
 **qcodes commit**

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,9 +1,30 @@
-Fixes #issuenumber.
+<!--
 
-Changes proposed in this pull request:
--
--
--
+Thanks for submitting a pull request against QCoDeS.
 
+To help us effectively merge your pr please consider the following check list.
 
-@mention one core developer
+- [ ] Make sure that the pull request contains a short description of the changes made.
+- [ ] If you are submitting a new feature please document it. This can be in the form of inline
+      docstrings, an example notebook or restructured text files.
+- [ ] Please include automatic tests for the changes made when possible.
+
+Unless your change is a small or trivial fix please add a small changelog entry:
+
+- [ ] Create a file in the docs\changes\newsfragments folder with a short description of the change.
+
+This file should be in the format number.categoryofcontribution. Here the number should either be the number
+of the pull request. To get the number of the pull request one must
+first the pull request and then subsequently update the number. The category of contribution should be
+one of ``breaking``, ``new``, ``improved``, ``new_driver`` ``improved_driver``, ``underthehood``.
+
+If this fixes a known bug reported against QCoDeS:
+
+- [ ] Please include a string in the following form ``closes #xxx`` where ``xxx``` is the number of the bug fixed.
+
+Please have a look at [the contributing guide](https://qcodes.github.io/Qcodes/community/contributing.html)
+for more information.
+
+If you are in doubt about any of this please ask and we will be happy to help.
+
+-->

.github/actions/prepare-cache-pip/action.yml

@@ -8,7 +8,7 @@ runs:
   using: "composite"
   steps:
     - name: upgrade pip setuptools wheel
-      run: pip install --upgrade pip setuptools wheel
+      run: python -m pip install --upgrade pip setuptools wheel
       shell: bash
     - name: Get pip cache dir
       id: get-pip-cache-dir

.github/dependabot.yml

@@ -5,7 +5,9 @@ updates:
   schedule:
     interval: daily
   open-pull-requests-limit: 10
+  rebase-strategy: "disabled"
 - package-ecosystem: github-actions
   directory: "/"
+  rebase-strategy: "disabled"
   schedule:
     interval: "daily"

.github/static/environment_forge_full.yml

@@ -6,19 +6,19 @@ dependencies:
  # recommended to be explicitly specified by conda-incubator/setup-miniconda@v2
  - pip
  # dependencies for setup.cfg
- - numpy>=1.15
+ - numpy>=1.17
  - pyvisa>=1.11.0, <1.12.0
  - h5py>=2.8.0
  - websockets>=7.0
  - jsonschema>=3.0.0
  - ruamel.yaml>=0.16.0,!=0.16.6
  - wrapt>=1.10.4
- - pandas>=0.25.0
- - xarray>=0.16.2
- - netCDF4>=1.5.0.1
+ - pandas>=1.0.0
+ - xarray>=0.18.0
+ - h5netcdf>=0.8.0
  - tabulate>=0.8.0
  - tqdm>=4.20.0
- - opencensus>=0.7.10, <0.8.0
+ - opencensus>=0.7.10, <0.9.0
  - opencensus-ext-azure>=1.0.4, <2.0.0
  - matplotlib>=2.2.3
  - requirements-parser>=0.2.0
@@ -27,6 +27,7 @@ dependencies:
  - packaging>=20.0
  - ipywidgets>=7.5.0
  - broadbean>=0.9.1
+ - uncertainties>=3.0.2
  # test requirements from setup.cfg
  - deepdiff>=5.0.2
  - hypothesis>=5.49.0
@@ -35,10 +36,15 @@ dependencies:
  - pytest-xdist>=2.0.0
  - pytest-mock>=3.0.0
  - lxml>=4.3.0
+ - sphinx
  # extra relevant requirements from setup.cfg
  - pyqtgraph>=0.11.0
  # for running mypy type checking
  - mypy
  - mypy_extensions
  - pip:
    - pyvisa-sim>=0.4.0  # required for testing
+   - versioningit>=0.3.0
+   - types-pkg_resources
+   - types_requests
+   - types-tabulate

.github/workflows/cancel_old_jobs.yaml

@@ -0,0 +1,14 @@
+name: Cancel old jobs
+on:
+  workflow_run:
+    workflows: ["build docs", "Run mypy and pytest", "Run pytest with minimum requirements", "run qcodes.pytest()", "Install all deps from conda-forge and run pytest"]
+    types:
+      - requested
+jobs:
+  cancel:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: styfle/cancel-workflow-action@0.9.1
+      with:
+        all_but_latest: true
+        workflow_id: ${{ github.event.workflow.id }}

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,36 @@
+name: "CodeQL"
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '42 15 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/conda-forge-install-and-test.yaml

@@ -5,12 +5,14 @@ on:
     branches:
       - 'master'
       - 'release/*'
+      - 'staging'
+      - 'trying'
     tags:
       - 'v*'
   pull_request:
 
 jobs:
-  build:
+  pytestconda:
 
     runs-on: ${{ matrix.os }}
     strategy:
@@ -22,14 +24,14 @@ jobs:
 
     steps:
     - name: checkout source code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v2.3.4
       with:
         submodules: true
     - name: setup ubuntu-latest xvfb
       uses: ./.github/actions/setup-ubuntu-latest-xvfb
       if: runner.os == 'Linux'
     - name: install dependencies
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v2.1.1
       with:
         activate-environment: qcodesforge
         environment-file: .github/static/environment_forge_full.yml

.github/workflows/docs.yaml

@@ -5,35 +5,39 @@ on:
     branches:
       - 'master'
       - 'release/*'
+      - 'staging'
+      - 'trying'
     tags:
       - 'v*'
   pull_request:
 
 jobs:
-  build:
+  builddocs:
 
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.7, 3.9, "3.10"]
         exclude:
-          - os: windows-latest
-            python-version: 3.8
           - os: windows-latest
             python-version: 3.9
+          - os: windows-latest
+            python-version: 3.10
+          - os: ubuntu-latest
+            python-version: 3.7
     env:
       DISPLAY: ':99.0'
       OS: ${{ matrix.os }}
-      UPLOAD_TO_GHPAGES: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.7' && github.event_name == 'push' && github.ref == 'refs/heads/master' }}
+      UPLOAD_TO_GHPAGES: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9' && github.event_name == 'push' && github.ref == 'refs/heads/master' }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v2.3.4
       with:
         fetch-depth: '0'
         # if we upload to ghpages we need the full
         # history to generate correct version info
       if: ${{ fromJSON(env.UPLOAD_TO_GHPAGES) }}
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v2.3.4
       if: ${{ !fromJSON(env.UPLOAD_TO_GHPAGES) }}
     - name: setup ubuntu-latest xvfb
       uses: ./.github/actions/setup-ubuntu-latest-xvfb
@@ -42,19 +46,23 @@ jobs:
       run: sudo apt install pandoc
       if: runner.os == 'Linux'
     - name: Install pandoc on windows
-      uses: crazy-max/ghaction-chocolatey@v1.4.0
+      uses: Wandalen/wretry.action@v1.0.12
       with:
-        args: install pandoc
+        action: crazy-max/ghaction-chocolatey@v1.6.0
+        with: |
+          args: install pandoc
+        attempt_limit: 5
+        attempt_delay: 1000
       if: runner.os == 'Windows'
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v2.3.1
       with:
         python-version: ${{ matrix.python-version }}
     - name: prepare pip cache
       id: prepare-cache-pip
       uses: ./.github/actions/prepare-cache-pip
     - name: pip cache
-      uses: actions/cache@v2.1.4
+      uses: actions/cache@v2.1.7
       with:
         path: ${{ steps.prepare-cache-pip.outputs.cache-dir }}
         key: ${{ runner.os }}-${{ matrix.python-version }}-pip-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/docs_requirements.txt') }}-${{ hashFiles('**/setup.cfg') }}
@@ -82,16 +90,17 @@ jobs:
         ./make.bat html
       if: runner.os == 'Windows'
     - name: Upload build docs
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v2.3.1
       with:
         name: docs_${{ matrix.python-version }}_${{ matrix.os }}
         path: ${{ github.workspace }}/docs/_build/html
     - name: Deploy to gh pages
-      uses: JamesIves/github-pages-deploy-action@4.1.0
+      uses: JamesIves/github-pages-deploy-action@v4.2.2
       with:
         branch: gh-pages
         folder: ${{ github.workspace }}/docs/_build/html
         clean: true
+        single-commit: true
         git-config-email: "bot"
         git-config-name: "Documentation Bot"
       if: ${{ fromJSON(env.UPLOAD_TO_GHPAGES) }}