Image comparison for testpackage outputs -> CI

.github/workflows/generate_reference_plots.yml

@@ -1,6 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
+# This workflow will install Python dependencies , analysator and generate verification set to /wrk-kappa/group/spacephysics/analysator/CI/verification_sets/ under new folder based on commit id
 name: generate_reference_data
 
 on:
@@ -43,9 +41,10 @@ jobs:
 
             DATAPATH="/wrk-kappa/group/spacephysics/analysator/CI/verification_sets/$(git rev-parse HEAD)"
             mkdir $DATAPATH
+            touch $DATAPATH/.lockfile
             sbatch -W -o testpackage_gen_verf.txt --job-name gen_verf_plots ./testpackage/run_testpackage_generate_verf_set.sh $DATAPATH
-
 
             cat testpackage_gen_verf.txt
 
             python ./testpackage/testpackage_get_job_error.py testpackage_gen_verf.txt
+            rm $DATAPATH/.lockfile

.github/workflows/test_compare_image_oldest_python.yml

@@ -26,15 +26,38 @@ jobs:
         - name: Get oldest allowed python version from pyproject.toml
           id: pyversion
           run: |
-            echo "PYTHON=$(cat pyproject | grep -Po '^requires-python\W*=\W*".+\K\d.+\d')" >> $GITHUB_OUTPUT
+            module purge
+            PYTHON=$(cat pyproject.toml | grep -Po '^requires-python\W*=\W*".+\K\d.+\d')
+            #PYTHON="3.7"
+            MAJOR=$(echo $PYTHON | grep -Po '^\d+')
+            MINOR=$(echo $PYTHON | grep -Po '\.\K\d+([\.]|$)')
+            AVAILABLE_VERSIONS=$(module spider Python)
+            N=0
+            while [[ ! $VERSIONS_MATCH ]]
+            do
+              echo "Trying to find module for Python/$PYTHON"
+              VERSIONS_MATCH=$(echo $AVAILABLE_VERSIONS | grep -Po 'Python/.+?-' | grep -Po 'Python'/$PYTHON)
+              if [[ ! $VERSIONS_MATCH ]]; then          
+                MINOR=$(( $MINOR + 1 ))
+                PYTHON=$MAJOR.$MINOR
+                N=$(( N + 1))
+                if (( N> 20 )); then
+                  echo "::error:: Could not find a python version to use."
+                  exit 1
+                fi
+              fi
+            done
+            echo "PYTHON=$PYTHON" >> $GITHUB_OUTPUT
             module load Python/$PYTHON
+            module list Python
         - name: Install dependencies
           timeout-minutes: 5
           run: |
             export TMPDIR=$RUNNER_TEMP
             export UV_LINK_MODE=copy
             module purge
-            module load Python/{{ steps.pyversion.outputs.PYTHON }}
+            module load Python/${{ steps.pyversion.outputs.PYTHON }}
+            module list
             uv venv CI_env
             . CI_env/bin/activate
             uv pip install --editable ../analysator[${{ matrix.extras }}]
@@ -43,7 +66,7 @@ jobs:
           run: |
             export TMPDIR=$RUNNER_TEMP
             module purge
-            module load Python/{{ steps.pyversion.outputs.PYTHON }}
+            module load Python/${{ steps.pyversion.outputs.PYTHON }}
             verf_loc="/wrk-kappa/group/spacephysics/analysator/CI/verification_sets"
             verfset=$(ls -lth $verf_loc | grep ^d | head -n1 | grep -Po '\w+$')
             if [[ -f $verf_loc/$verfset/.lockfile ]]; then 
@@ -59,7 +82,7 @@ jobs:
         - name: Comparing plotted data
           run: |
             export TMPDIR=$RUNNER_TEMP
-            module load Python/{{ steps.pyversion.outputs.PYTHON }}
+            module load Python/${{ steps.pyversion.outputs.PYTHON }}
             . CI_env/bin/activate
             sbatch -W -o "testpackage_compare.txt" ./testpackage/run_compare.sh
             cat testpackage_compare.txt

.github/workflows/test_compare_images.yml

@@ -1,9 +1,9 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
+# This workflow will install Python dependencies and analysator, run the analysator testpackage based on git diff and compare the images 
 name: Turso compare selectively images
 
 on:
+  pull_request:
+    branches: [ master, dev]
   workflow_dispatch:
 
 concurrency:
@@ -21,7 +21,7 @@ jobs:
           fail-fast: false
           max-parallel: 2
           matrix:
-            extras: ["all"]
+            extras: ["testpackage"]
         steps:
         - uses: actions/checkout@v4
           timeout-minutes: 5
@@ -46,10 +46,18 @@ jobs:
             export TMPDIR=$RUNNER_TEMP
             module purge
             module load Python/3.10.4-GCCcore-11.3.0
-
-            export DIFFRESULT=$(python ./testpackage/testpackage_get_diff.py)
+            verf_loc="/wrk-kappa/group/spacephysics/analysator/CI/verification_sets"
+            verfset=$(ls -lth $verf_loc | grep ^d | head -n1 | grep -Po '\w+$')
+            if [[ -f $verf_loc/$verfset/.lockfile ]]; then 
+              echo -e ".lockfile found in $verf_loc/$verfset, not running test, as the verification set generation is likely still ongoing\n Check ongoing actions and/or re-run verification set generation."
+              exit 1
+            fi
+            export DIFFRESULT=$(python ./testpackage/testpackage_get_diff.py ${{ github.base_ref }})
+            if [[ -f diff_log.txt ]]; then
+              cat diff_log.txt
+            fi
             echo "DIFFRESULT=$DIFFRESULT" >> $GITHUB_OUTPUT
-            echo "$DIFFRESULT"
+            echo "Running $DIFFRESULT"
             sbatch -W -o testpackage_run.txt --job-name gen_plots ./testpackage/run_testpackage_workflow.sh $DIFFRESULT
 
             cat testpackage_run.txt

.github/workflows/test_compare_images_full.yml

@@ -1,15 +1,14 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+#This workflow will install python and run the full analysator testpackage with image comparison for the results
 
 name: Turso compare all images
 
 on:
+  push:
+    branches: [ master, dev]
+  schedule:
+    - cron: '0 8 * * MON'
   workflow_dispatch:
 
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
-
 
 jobs:
 
@@ -21,7 +20,7 @@ jobs:
           fail-fast: false
           max-parallel: 2
           matrix:
-            extras: ["all"]
+            extras: ["testpackage"]
         steps:
         - uses: actions/checkout@v4
           timeout-minutes: 5
@@ -44,7 +43,12 @@ jobs:
             export TMPDIR=$RUNNER_TEMP
             module purge
             module load Python/3.10.4-GCCcore-11.3.0
-
+            verf_loc="/wrk-kappa/group/spacephysics/analysator/CI/verification_sets"
+            verfset=$(ls -lth $verf_loc | grep ^d | head -n1 | grep -Po '\w+$')
+            if [[ -f $verf_loc/$verfset/.lockfile ]]; then 
+              echo -e ".lockfile found in $verf_loc/$verfset, not running test, as the verification set generation is likely still ongoing\n Check ongoing actions and/or re-run verification set generation."
+              exit 1
+            fi 
             sbatch -W -o testpackage_run.txt --job-name gen_plots ./testpackage/run_testpackage_workflow.sh
 
             cat testpackage_run.txt

.github/workflows/test_python_turso.yml

@@ -23,9 +23,12 @@ jobs:
             extras: ["none", "all", "bvtk"]
         steps:
         - uses: actions/checkout@v4
+          timeout-minutes: 5
         - name: Install uv
           uses: astral-sh/setup-uv@v6
+          timeout-minutes: 5
         - name: Install dependencies
+          timeout-minutes: 5
           run: |
             export TMPDIR=$RUNNER_TEMP
             uv venv CI_env

analysator/pyPlots/plot_vdf.py

@@ -427,7 +427,7 @@ def plot_vdf(filename=None,
              biglabel=None, biglabloc=None,
              noxlabels=None, noylabels=None,
              axes=None, cbaxes=None, cb_horizontal=False,
-             contours=None
+             contours=None,figsize=None
              ):
 
     ''' Plots a coloured 2D plot of a VDF (a slice of given thickness or fully projected) with axes and a colour bar.
@@ -521,7 +521,7 @@ def plot_vdf(filename=None,
     :kword scale_cb:    Colour bar text additional scale factor (default=5.0)
     :kword scale_label: Big label text additional scale factor (default=12.0)
     :kword thick:       line and axis thickness, default=1.0
-
+    :kword figsize:     Set figure size, default=None which will use [4.0,3.15*ratio]
 
     :returns:           Outputs an image to a file or to the screen.
 
@@ -1080,15 +1080,21 @@ def plot_vdf(filename=None,
         # Define figure size
         ratio = (yvalsrange[1]-yvalsrange[0])/(xvalsrange[1]-xvalsrange[0])
         # default for square figure is figsize=[4.0,3.15]
-        figsize = [4.0,3.15*ratio]
 
         # Plot the slice
         [XmeshXY,YmeshXY] = np.meshgrid(edgesX/velUnit,edgesY/velUnit) # Generates the mesh to map the data to
 
         if axes is None:
-            # Create 300 dpi image of suitable size
-            fig = plt.figure(figsize=figsize,dpi=300)
+            if figsize is not None:
+
+                if noborder: 
+                    logging.warning("noborder and figsize enabled, this may undo effects of figsize")
+                fig = plt.figure(figsize=figsize,dpi=300)
+            else:
+                # Create 300 dpi image of suitable size
+                fig = plt.figure(figsize=[4.0,3.15*ratio] ,dpi=300)
             ax1 = plt.gca() # get current axes
+
         else:
             ax1=axes
         fig1 = ax1.pcolormesh(XmeshXY,YmeshXY,binsXY, cmap=colormap,norm=norm)
@@ -1176,8 +1182,7 @@ def plot_vdf(filename=None,
             elif biglabloc==3:
                 BLcoords=[0.02,0.02]
                 BLha = "left"
-                BLva = "bottom"
-
+                BLva = "bottom" 
             plt.text(BLcoords[0],BLcoords[1],biglabel, fontsize=fontsize4,weight='black', transform=ax1.transAxes, ha=BLha, va=BLva,color='k',bbox=dict(facecolor='white', alpha=0.5, edgecolor=None))
 
 
@@ -1295,6 +1300,9 @@ def plot_vdf(filename=None,
             plt.tight_layout()
             savefig_pad=0.05 # The default is 0.1
             bbox_inches=None
+        elif figsize is not None:
+            savefig_pad=0.05
+            bbox_inches=None
         else:
             plt.tight_layout(pad=0.01)
             savefig_pad=0.01

pyproject.toml

@@ -39,7 +39,10 @@ all = [
 bvtk = [
     "vtk==9.2.6",
 ]
-
+testpackage = [
+    "opencv-python",
+    "analysator[vtk]",
+]
 [project.urls]
 Homepage = "https://github.com/fmihpc/analysator"
 Issues = "https://github.com/fmihpc/analysator/issues"

testpackage/create_env.py

@@ -0,0 +1,90 @@
+import os
+import venv
+from testpackage_helpers import system_call
+from sys import version_info as python_version_info
+from sys import version as python_version
+import argparse
+
+def create_venv(path,install_analysator=True,editable=False):
+    virt_env= venv.EnvBuilder(with_pip=True,upgrade_deps=True)
+    context=virt_env.ensure_directories(path)
+    virt_env.create(path)
+    virt_env.setup_python(context)
+
+    #Does not work in python versions <3.13
+    if python_version_info.major>=3 and python_version_info.minor>=13:
+        virt_env.create_git_ignore_file(context)
+
+    virt_env.create_configuration(context)
+    virt_env.setup_scripts(context)
+    virt_env.post_setup(context)
+    if install_analysator:
+        editable='--editable' if editable else None
+        system_call(f'{path}/bin/pip install {editable} ../[testpackage]',live_output=True)
+    print(f'Virtual environment created at {path}')
+    return None
+
+
+def create_venv_script(path,venv_path):
+    if path[-1]!="/":
+        path=path+"/"
+
+    if not os.path.isdir(path):
+        raise FileNotFoundError(f"{path} does not exist.")
+
+    if os.path.isfile(path+"pyvenv.sh"):
+        #If file exists, check for source line and add one if not present
+        with open(path+"pyvenv.sh","a+") as f:
+            f.seek(0)
+            for line in f:
+                if "source" in line[:6]:
+                    raise SystemError("source line already in pyvenv.sh!")
+
+            f.write(f"source {venv_path}/bin/activate\n")
+            f.close()
+    else:
+        #Create the file with the source line
+        with open(path+"pyvenv.sh","w") as f:
+            f.write("module purge\n")
+            if 'TURSO' in os.uname().nodename.upper():
+                f.write("export PATH=/wrk-vakka/group/spacephysics/proj/appl/tex-basic/texlive/2023/bin/x86_64-linux:$PATH\n")
+
+            #Get used python version and gcc version
+            #note that this may break if the version string format changes
+            #Module load of python is required, otherwise python cannot be called outside the directory the venv is in (if the module system is used)
+            version_info = python_version.split(" ")
+            used_python_version = version_info[0]
+            used_gcc_version = version_info[-1].strip("[]")
+
+            #If module system is used, on HILE use cray-python!
+            if 'HILE' in os.uname().nodename.upper():
+                f.write("module load cray-python\n")
+            else:
+                f.write(f"module load Python/{used_python_version}-GCCcore-{used_gcc_version}\n")
+            f.write("module list\n")
+            f.write(f"source {venv_path}/bin/activate\n")
+
+            f.close()
+
+
+if __name__ == "__main__":
+    #Will install python venv with same version as the python this script was called with 
+
+    create_venv_local = True        #Create a virtual environment in the current folder (should be in testpackage folder)
+
+    parser=argparse.ArgumentParser(description='Create python virtual environment for testpackage, will also create batch script that can be sourced.')
+    parser.add_argument('--no-analysator',action='store_true',help='Do not install analysator.',default=False)
+    parser.add_argument('--editable','-e',action='store_true',help='Install analysator as editable',default=True)
+    args=parser.parse_args()
+
+    venv_name= 'venv_testpackage'
+    venv_path = os.path.abspath('./'+venv_name)
+    if venv_name not in os.listdir('.') and create_venv_local:
+        print('venv_testpackage not found, creating virtual environment')
+        create_venv(venv_path,editable=args.editable,install_analysator=not args.no_analysator)
+        create_venv_script('./',venv_path)
+    else:
+        print('venv_testpackage found, not creating virtual environment')
+
+
+