Merge pull request #131 from q-optimize/release/1.3

Release/1.3

.github/ISSUE_TEMPLATE/bug_report.md

@@ -7,32 +7,22 @@ assignees: ''
 
 ---
 
-**Describe the bug**
+## Describe the bug
 A clear and concise description of what the bug is.
 
-**To Reproduce**
-Steps to reproduce the behavior:
-1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
-4. See error
+## To Reproduce
+Steps to reproduce the behavior. This can be in the form of a code snippet or some config files or a notebook to produce a minimum viable example of the bug.
 
-**Expected behavior**
-A clear and concise description of what you expected to happen.
+## Expected behavior
+A clear and concise description of what you expect(ed) to happen.
 
-**Screenshots**
+## Screenshots
 If applicable, add screenshots to help explain your problem.
 
-**Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
+## Environment (please complete the following information)
+ - OS: [e.g. MacOS]
+ - Python Version: [e.g. 3.8]
+ - `c3-toolset` Version [e.g. 1.2]
 
-**Smartphone (please complete the following information):**
- - Device: [e.g. iPhone6]
- - OS: [e.g. iOS8.1]
- - Browser [e.g. stock browser, safari]
- - Version [e.g. 22]
-
-**Additional context**
-Add any other context about the problem here.
+## Additional context
+Add any other context about the problem here. You can also suggest possible solutions and relevant implementations & edge case details.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -7,14 +7,14 @@ assignees: ''
 
 ---
 
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+## Describe the missing feature
+A clear and concise description of what the problem is and what is being missed. Ex. I'm always frustrated when [...]
 
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen.
+## Describe the solution you'd like
+A clear and concise description of what you want to happen. If possible, provide example input-output descriptions or usecases. Better still, consider providing code snippets that outline the expected behaviour. Ex. I would like to call [...] on the [...] class objects to get [...] done.
 
-**Describe alternatives you've considered**
-A clear and concise description of any alternative solutions or features you've considered.
+## Describe alternatives you've considered
+How have you tried to resolve it in the current version of the code? Have you considered non `c3-toolset` alternative solutions? Please elaborate.
 
-**Additional context**
-Add any other context or screenshots about the feature request here.
+## Additional context
+Add any other context or screenshots about the feature request here. Please feel free to suggest details about how you believe this feature request might be best implemented. If you have used similar features in other libraries, consider providing links or resources to example implementations.

.github/prepare-nightly.py

@@ -2,24 +2,24 @@
 import os
 import re
 
-_PATH_INIT = os.path.join(os.getcwd(), 'c3', '__init__.py')
-_PATH_SETUP = os.path.join(os.getcwd(), 'setup.py')
+_PATH_INIT = os.path.join(os.getcwd(), "c3", "__init__.py")
+_PATH_SETUP = os.path.join(os.getcwd(), "setup.py")
 
 # get today date
 now = datetime.datetime.now()
 now_date = now.strftime("%Y%m%d")
 
 print(f"Update init - replace version by {now_date}")
-with open(_PATH_INIT, 'r') as fp:
+with open(_PATH_INIT, "r") as fp:
     init = fp.read()
 init = re.sub(r'__version__ = [\d\.\w\'"]+', f'__version__ = "{now_date}"', init)
-with open(_PATH_INIT, 'w') as fp:
+with open(_PATH_INIT, "w") as fp:
     fp.write(init)
 
 print(f"Update setup - replace version by {now_date} and update to c3-toolset-nightly")
-with open(_PATH_SETUP, 'r') as fp:
+with open(_PATH_SETUP, "r") as fp:
     setup = fp.read()
 setup = re.sub(r'version=[\d\.\w\'"]+', f'version="{now_date}"', setup)
-setup = re.sub(r'name="c3-toolset"', f'name="c3-toolset-nightly"', setup)
-with open(_PATH_SETUP, 'w') as fp:
-    fp.write(setup)
+setup = re.sub(r'name="c3-toolset"', 'name="c3-toolset-nightly"', setup)
+with open(_PATH_SETUP, "w") as fp:
+    fp.write(setup)

.github/pull_request_template.md

@@ -0,0 +1,22 @@
+## What
+Describe very concisely what this Pull Request does. 
+
+## Why
+Describe what motivated this Pull Request and why this was necessary. Use closing keywords to link to the relevant Issue. Ex. Closes #666
+
+## How
+Describe details of how you implemented the solution, outlining the major steps involved in adding this new feature or fixing this bug. Provide code-snippets if possible, showing example usage.
+
+## Remarks
+Add notes on possible known quirks/drawbacks of this solution. If this introduces an API-breaking change, please provide an explanation on why it is necessary to break API compatibility and how users should update their notebook/script workflows once this PR is merged.
+
+## Checklist
+Please include and complete the following checklist. Your Pull Request is (in most cases) not ready for review until the following have been completed. You can create a draft PR while you are still completing the checklist. Check the [Contribution Guidelines](https://github.com/q-optimize/c3/blob/dev/CONTRIBUTING.md) for more details. You can mark an item as complete with the `- [x]` prefix
+
+- [ ] Tests - Added unit tests for new code, regression tests for bugs and updated the integration tests if required
+- [ ] Formatting & Linting - `black` and `flake8` have been used to ensure styling guidelines are met
+- [ ] Type Annotations - All new code has been type annotated in the function signatures using type hints
+- [ ] Docstrings - Docstrings have been provided for functions in the `numpydoc` style
+- [ ] Documentation - The tutorial style documentation has been updated to explain changes & new features
+- [ ] Notebooks - Example notebooks have been updated to incorporate changes and new features
+- [ ] Changelog - A short note on this PR has been added to the Upcoming Release section

.github/workflows/build_package.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04, ubuntu-18.04, macos-latest, windows-latest]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python-version }}
@@ -26,16 +26,9 @@ jobs:
     - name: Install c3 package
       run: |
         python -m pip install --upgrade pip
-        pip install pytest-cov qiskit==0.23.2
+        pip install pytest qiskit==0.25.0
         pip install .
     - name: Test with pytest
       run: |
-        pytest -v --cov=c3 --cov-report=xml test/
-    - name: Upload build stats to Codecov
-      uses: codecov/codecov-action@v1
-      with:
-        file: ./coverage.xml
-        env_vars: OS,PYTHON
-        name: build-c3
-        fail_ci_if_error: false
-        verbose: true
+        pytest -v -x -m "not slow" test/
+        pytest -v -x -m "slow" test/

.github/workflows/coverage.yml

@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  coverage_check_upload:
 
     runs-on: ubuntu-latest
     strategy:
@@ -29,7 +29,7 @@ jobs:
         pip install -r requirements.txt
     - name: Test with pytest
       run: |
-        pytest -v --cov=c3 --cov-report=xml test/
+        pytest -x -v --cov=c3 --cov-report=xml test/
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
       with:

.github/workflows/complexity.yml → .github/workflows/format_lint.yml

@@ -1,4 +1,4 @@
-name: Code Complexity
+name: Code Formatting and Linting
 
 on:
   push:
@@ -8,7 +8,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  format_lint_check:
 
     runs-on: ubuntu-latest
     strategy:
@@ -26,7 +26,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-    - name: Test Complexity with Xenon
+        pip install black flake8
+    - name: Test Code Formatting with Black
       run: |
-        xenon --max-absolute B --max-modules B --max-average A c3/
+        black --check c3/
+    - name: Code Linting with flake8
+      run: |
+        flake8 --count c3/
+

.github/workflows/integration_test.yml

@@ -8,12 +8,12 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  integration_unit_tests:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-20.04, ubuntu-18.04, macos-latest, windows-latest]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python-version }}
@@ -29,4 +29,5 @@ jobs:
         pip install -r requirements.txt
     - name: Test with pytest
       run: |
-        pytest -v --cov=c3 test/
+        pytest -v -x -m "not slow" test/
+        pytest -v -x -m "slow" test/

.github/workflows/nightly_pypi.yml

@@ -49,7 +49,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04, ubuntu-18.04, macos-latest, windows-latest]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python-version }}

.github/workflows/notebook_test.yml

@@ -0,0 +1,34 @@
+name: Notebook Test
+
+on:
+  push:
+    branches: [ master, dev, 'release/*' ]
+  pull_request:
+    branches: [ master, dev, 'release/*' ]
+  workflow_dispatch:
+
+jobs:
+  notebook_run_check:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.8]
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python-version }}
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install jupyter notebook ipykernel matplotlib
+        pip install .
+    - name: Test with nbconvert
+      run: |
+        jupyter nbconvert --to notebook --inplace --execute examples/*.ipynb

.github/workflows/publish_pypi.yml

@@ -45,7 +45,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04, ubuntu-18.04, macos-latest, windows-latest]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9]
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python-version }}

.gitignore

@@ -137,3 +137,5 @@ dmypy.json
 
 # swp files
 *.swp
+.stignore
+okteto.yml

.pre-commit-config.yaml

@@ -1,23 +1,22 @@
 repos:
 -   repo: https://github.com/ambv/black
-    rev: stable
+    rev: 21.5b1
     hooks:
     - id: black
-      language_version: python3.8
--   repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.3
+      language_version: python3
+-   repo: https://github.com/pycqa/flake8
+    rev: 3.9.2
     hooks:
     - id: flake8
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v0.790'
+    rev: 'v0.812'
     hooks:
     - id: mypy
       args: [--no-strict-optional, --ignore-missing-imports]
       additional_dependencies: [cma==3.0.3,
-                                matplotlib==3.3.2,
-                                numpy==1.18.5, 
+                                numpy==1.19.5, 
                                 scipy==1.5.2,
-                                tensorflow==2.3.1, 
-                                tensorflow-probability==0.11.1, 
-                                tensorflow-estimator==2.3.0
+                                tensorflow==2.4.2, 
+                                tensorflow-probability==0.12.1, 
+                                tensorflow-estimator==2.4.0
                                 ]

AUTHORS

@@ -3,4 +3,5 @@ Nicolas Wittler
 Shai Machnes
 Kevin Pack
 Anurag Saha Roy
+Niklas J Glaser
 Max Werninghaus