Update version numbers, include small improvements in pipelines (#127)

.github/workflows/codeql-analysis.yml

@@ -39,6 +39,8 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v2
+      with:
+        lfs: false
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/conda-installation-not-in-path.yaml

@@ -20,6 +20,8 @@ jobs:
       uses: fkirc/[email protected]
 
     - uses: actions/checkout@v2
+      with:
+        lfs: false
 
     - name: Install miniconda
       run: |

.github/workflows/conda-installation.yaml

@@ -20,6 +20,8 @@ jobs:
       uses: fkirc/[email protected]
 
     - uses: actions/checkout@v2
+      with:
+        lfs: false
 
     - uses: conda-incubator/setup-miniconda@v2
       with:

.github/workflows/demo.yaml

@@ -26,6 +26,8 @@ jobs:
       uses: fkirc/[email protected]
 
     - uses: actions/checkout@v2
+      with:
+        lfs: false
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2

.github/workflows/docs.yaml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9, "3.10"]
+        python-version: [3.8, "3.10"]  # Check the oldest and newest currently supported Python versions
 
     steps:
 

.github/workflows/installation-from-remote.yaml

@@ -23,6 +23,8 @@ jobs:
       uses: fkirc/[email protected]
 
     - uses: actions/checkout@v2
+      with:
+        lfs: false
 
     - uses: conda-incubator/setup-miniconda@v2
       with:
@@ -49,6 +51,8 @@ jobs:
       uses: fkirc/[email protected]
 
     - uses: actions/checkout@v2
+      with:
+        lfs: false
 
     - uses: conda-incubator/setup-miniconda@v2
       with:
@@ -84,10 +88,12 @@ jobs:
       uses: fkirc/[email protected]
 
     - uses: actions/checkout@v2
+      with:
+        lfs: false
 
     - uses: actions/setup-python@v4
       with:
-        python-version: '3.9'
+        python-version: '3.10'
 
     - name: Install ConFlowGen
       run: |

.github/workflows/linting.yml

@@ -11,7 +11,7 @@ on:
 
 jobs:
   build:
-    name: Check code quality with pylint and flake8
+    name: Check code quality with pylint, flake8, and flake8_nb
     runs-on: ubuntu-latest
 
     strategy:
@@ -25,6 +25,8 @@ jobs:
       uses: fkirc/[email protected]
 
     - uses: actions/checkout@v2
+      with:
+        lfs: false
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2

.github/workflows/unittests.yaml

@@ -20,11 +20,13 @@ jobs:
       uses: fkirc/[email protected]
 
     - uses: actions/checkout@v2
+      with:
+        lfs: false
 
-    - name: Set up Python 3.8
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: "3.10"
 
     - name: Install Python dependencies
       run: |

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.9"
+    python: "3.10"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

docs/conf.py

@@ -20,7 +20,7 @@
 from matplotlib.font_manager import fontManager
 fontManager.get_default_size()  # just some random action so that the import is not flagged as unnecessary
 
-# include conflowgen from source code, avoid getting served an outdated installation
+# include conflowgen from source code, avoid being served an outdated installation
 sys.path.insert(
     0,
     os.path.abspath(
@@ -176,14 +176,17 @@ def _install_git_lfs_on_linux_on_the_fly() -> str:
         return _git_lfs_cmd
 
     os.system("echo 'Installing git-lfs on-the-fly'")
-    version = 'v3.0.2'
+    version = 'v3.2.0'
     file_to_download = f'git-lfs-linux-amd64-{version}.tar.gz'
+    folder_inside_file = f"git-lfs-{version[1:]}"
     if not os.path.isfile(file_to_download):
         os.system(
             f'wget https://github.com/git-lfs/git-lfs/releases/download/{version}/{file_to_download}'
         )  # download git lfs
-    os.system(f'tar xvfz git-lfs-linux-amd64-{version}.tar.gz -C ./.tools')  # extract to ./.tools subdirectory
-    os.system('cp ./.tools/git-lfs ./git-lfs')  # take command (don't care about readme etc.)
+    os.system(f'tar xvfz {file_to_download} -C ./.tools')  # extract to ./.tools subdirectory
+    os.system(f'ls ./.tools/')
+    os.system(f'ls ./.tools/{folder_inside_file}')
+    os.system(f'cp ./.tools/{folder_inside_file}/git-lfs ./git-lfs')  # take command (don't care about readme etc.)
     os.system('./git-lfs install')  # make lfs available in current repository
     os.system("echo 'git-lfs is installed'")
     return _git_lfs_cmd

run_ci_light.bat

@@ -1,19 +1,53 @@
 @ECHO OFF
 
+ECHO.
 ECHO.Please run this batch script as a substitute of the GitHub workflows before creating a pull request. This light
 ECHO.version does not run the following CI pipelines:
 ECHO.- CodeQL analysis (only used by GitHub)
-ECHO.- Installing ConFlowGen in a fresh conda environment (not suitable for repeated invocation)
+ECHO.- Installing ConFlowGen from source in a fresh conda environment (not suitable for repeated invocation)
+ECHO.
+ECHO.This script needs to be invoked in the development environment, e.g., a virtual environment or a conda
+ECHO.environment.
 ECHO.
-ECHO.This script needs to be invoked in the development environment (e.g., a virtual environment or a conda
-ECHO.environment).
 
-REM run tests
-python -m pytest --exitfirst --verbose --failed-first --cov="./conflowgen" --cov-report html || ECHO.Tests failed && EXIT /B
+ECHO.The following Python interpreter is used:
+python -c "import sys; print(sys.base_prefix)"
+
+ECHO.The following sys.prefix is used (typically overwritten by the isolated environment you operate in):
+python -c "import sys; print(sys.prefix)"
+ECHO.
+
+IF "%VIRTUAL_ENV%" NEQ "" (
+    ECHO.Operating inside the virtual environment %VIRTUAL_ENV%
+    GOTO START_PIPELINE
+)
+
+IF "%CONDA_PREFIX%" NEQ "" (
+    ECHO.Operating inside the conda environment %CONDA_PREFIX%
+    GOTO START_PIPELINE
+)
 
-REM try installation process - as a developer this is the default installation anyways
+ECHO.It seems like you are not in an isolated development environment. In a later step, the current version of
+ECHO.ConFlowgen will be installed as a library. Please abort if you do not want to clutter your Python installation.
+ECHO.If you actually are in an isolated development environment, feel free to improve this check.
+
+:AGAIN
+ECHO.
+set /p answer="Continue anyway (Y/N)? "
+if /i "%answer:~,1%" EQU "Y" goto START_PIPELINE
+if /i "%answer:~,1%" EQU "N" exit /b
+ECHO.Please type Y for Yes or N for No
+GOTO AGAIN
+
+
+:START_PIPELINE
+REM Try the installation process - as a developer this is the default installation anyway
+REM This also ships the commands that are used in the latter stages of the pipeline
 python -m pip install -e .[dev] || ECHO.Installation failed && EXIT /B
 
+REM run tests
+python -m pytest --exitfirst --verbose --failed-first --cov="./conflowgen" --cov-report html || ECHO.Tests failed && EXIT /B
+
 REM check code quality
 flake8 || ECHO.While linting, flake8 failed && EXIT /B
 flake8_nb || ECHO.While linting, flake8_nb failed && EXIT /B