Merge branch 'devel' into cuda_main

.dict_custom.txt

@@ -64,6 +64,7 @@ RedBaron
 intel
 nvidia
 boolean
+booleans
 quicksort
 iterm
 textx

.docstr_coverage

@@ -0,0 +1,3 @@
+.*code _print_.*
+semantic _visit_.*
+syntactic _visit_.*

.github/actions/coverage_collection/action.yml

@@ -1,4 +1,9 @@
 name: 'Coverage Collection'
+inputs:
+  shell_cmd:
+    description: 'Specifies the shell command (different for anaconda)'
+    required: false
+    default: 'bash'
 
 runs:
   using: "composite"
@@ -7,5 +12,5 @@ runs:
       run: |
         coverage combine
         rm ${SITE_DIR}/pyccel_cov.pth
-      shell: bash
+      shell: ${{ inputs.shell_cmd }}
 

.github/actions/coverage_install/action.yml

@@ -1,12 +1,17 @@
 name: 'Coverage Setup'
+inputs:
+  shell_cmd:
+    description: 'Specifies the shell command (different for anaconda)'
+    required: false
+    default: 'bash'
 
 runs:
   using: "composite"
   steps:
     - name: Installation
       run: |
         python -m pip install coverage
-      shell: bash
+      shell: ${{ inputs.shell_cmd }}
     - name: Directory Creation
       run: |
         INSTALL_DIR=$(cd tests; python -c "import pyccel; print(pyccel.__path__[0])")
@@ -15,4 +20,4 @@ runs:
         echo -e "[run]\nparallel = True\nsource = ${INSTALL_DIR}\ndata_file = $(pwd)/.coverage\n[report]\ninclude = ${INSTALL_DIR}/*\n[xml]\noutput = cobertura.xml" > .coveragerc
         echo "SITE_DIR=${SITE_DIR}" >> $GITHUB_ENV
         echo "COVERAGE_PROCESS_START=$(pwd)/.coveragerc" >> $GITHUB_ENV
-      shell: bash
+      shell: ${{ inputs.shell_cmd }}

.github/actions/generate_bot_token/action.yml

@@ -0,0 +1,23 @@
+name: "Generate bot token"
+inputs:
+  bot_pem:
+    description: "The private key which identifies the bot"
+    required: true
+  dir:
+    description: "The directory where the code is found"
+    required: false
+    default: "."
+
+runs:
+  using: "composite"
+  steps:
+    - run: |
+        pip install jwt requests
+      shell: bash
+    - run: |
+        cd ${{ inputs.dir }}
+        python -c "from ci_tools.bot_tools.github_api_interactions import get_authorization; t,d=get_authorization(); print('token=',t,sep=''); print('token_exp=',d,sep='')"
+      shell: bash
+      id: get_token
+      env:
+        PEM: ${{ inputs.bot_pem }}

.github/actions/post_completed/action.yml

@@ -0,0 +1,34 @@
+name: 'Posting in progress status'
+inputs:
+  installation_token:
+    description: "The GitHub API token of the bot"
+    required: true
+  run_id:
+    description: "The id of the check run"
+    required: true
+  status:
+    description: "The final status of the workflow"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: "Collecting status"
+      run: |
+        import os
+        import json
+        import requests
+        if os.path.exists('test_json_result.json'):
+            with open('test_json_result.json', 'r') as f:
+                result = json.load(f)
+        else:
+            result = {}
+        result["status"] = "completed"
+        result["conclusion"] = "${{ inputs.status }}"
+
+        headers = {"Accept": "application/vnd.github+json", "Authorization": "Bearer ${{ inputs.installation_token }}", "X-GitHub-Api-Version": "2022-11-28"}
+
+        reply = requests.patch("https://api.github.com/repos/${{ github.repository }}/check-runs/${{ inputs.run_id }}", headers=headers, json=result)
+
+        print(reply.text)
+      shell: python

.github/actions/post_triggered/action.yml

@@ -0,0 +1,39 @@
+name: 'Posting in progress status'
+inputs:
+  ref:
+    description: "The ref to post the status to"
+    required: true
+  installation_token:
+    description: "The GitHub API token of the bot"
+    required: true
+  name:
+    description: "The name of the workflow"
+    required: true
+outputs:
+  check_id:
+    description: "The ID of the check run"
+    value: ${{ steps.post.outputs.check_id }}
+
+runs:
+  using: "composite"
+  steps:
+    - name: "Posting"
+      run: |
+        import requests
+        
+        headers = {"Accept": "application/vnd.github+json", "Authorization": "Bearer ${{ inputs.installation_token }}", "X-GitHub-Api-Version": "2022-11-28"}
+        data = {"name":"${{ inputs.name }}",
+                "head_sha":"${{ inputs.ref }}",
+                "status":"in_progress",
+                "details_url": "https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}"}
+
+        reply = requests.post("https://api.github.com/repos/${{ github.repository }}/check-runs", headers=headers, json=data)
+
+        print(reply.text)
+        print(reply.json())
+
+        id = reply.json()["id"]
+        with open("${{ github.output }}", 'a') as f:
+            print("check_id=", id, sep='', file=f)
+      shell: python
+      id: post

.github/actions/pytest_run/action.yml

@@ -13,30 +13,72 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - name: Test with pytest
+    - name: Set up runner
       run: |
         which python
         if [ -n "${{ runner.debug }}" ]
         then
           # If running in debug mode
-          export "DEBUG=1"
+          echo "DEBUG=1" >> $GITHUB_ENV
           export FLAGS="-xsv --log-cli-level DEBUG"
         else
           export FLAGS=""
         fi
-        python -m pytest -n auto -rXx ${FLAGS} -m "not (parallel or xdist_incompatible) and c ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays
-        if [ -n "${SITE_DIR}" ]; then
+        echo "FLAGS=${FLAGS}" >> $GITHUB_ENV
+      shell: ${{ inputs.shell_cmd }}
+      working-directory: ./tests
+    - name: Pytest with options (1)
+      run: python -m pytest -n auto -rXx ${FLAGS} -m "not (parallel or xdist_incompatible) and c ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays 2>&1 | tee s1_outfile.out
+      shell: ${{ inputs.shell_cmd }}
+      working-directory: ./tests
+      id: pytest_1
+    - name: if SITE_DIR is set (2)
+      run: |
+         if [ -n "${SITE_DIR}" ]; then
             echo "Touching"
             # Test ndarray folder update (requires parallel tests to avoid clean)
             touch ${SITE_DIR}/pyccel/stdlib/cwrapper/cwrapper.h
-            python -m pytest -n auto -rXx ${FLAGS} -m c -k test_array_int32_1d_scalar epyccel/test_arrays.py
+            python -m pytest -n auto -rXx ${FLAGS} -m c -k test_array_int32_1d_scalar epyccel/test_arrays.py 2>&1 | tee s2_outfile.out
         fi
-        python -m pytest -rXx ${FLAGS} -m "xdist_incompatible and not parallel and c ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays
-        pyccel-clean
-        python -m pytest -n auto -rXx ${FLAGS} -m "not (parallel or xdist_incompatible) and not (c or python or ccuda) ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays
-        python -m pytest -rXx ${FLAGS} -m "xdist_incompatible and not parallel and not (c or python or ccuda) ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays
+      shell: ${{ inputs.shell_cmd }}
+      working-directory: ./tests
+      id: pytest_2
+    - name: pytest with options (3)
+      run: |
+         python -m pytest -rXx ${FLAGS} -m "xdist_incompatible and not parallel and c ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays 2>&1 | tee s3_outfile.out
+         pyccel-clean
+      shell: ${{ inputs.shell_cmd }}
+      working-directory: ./tests
+      id: pytest_3
+    - name: pytest with options (4)
+      run: python -m pytest -n auto -rXx ${FLAGS} -m "not (parallel or xdist_incompatible) and not (c or python or ccuda) ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays 2>&1 | tee s4_outfile.out
+      shell: ${{ inputs.shell_cmd }}
+      working-directory: ./tests
+      id: pytest_4
+    - name: pytest with options (5)
+      run: |
+        python -m pytest -rXx ${FLAGS} -m "xdist_incompatible and not parallel and not (c or python or ccuda) ${{ inputs.pytest_mark }}" --ignore=symbolic --ignore=ndarrays | tee s5_outfile.out
         pyccel-clean
-        python -m pytest ndarrays/ -rXx ${FLAGS}
+      shell: ${{ inputs.shell_cmd }}
+      working-directory: ./tests
+      id: pytest_5
+    - name: pytest ndarrays (6)
+      run: |
+        python -m pytest ndarrays/ -rXx ${FLAGS} 2>&1 | tee s6_outfile.out
         pyccel-clean
       shell: ${{ inputs.shell_cmd }}
       working-directory: ./tests
+      id: pytest_6
+    - name: Final step
+      if: always()
+      id: status
+      run:
+        python ci_tools/json_pytest_output.py -t "Linux Test Summary" --tests "C tests:${{ steps.pytest_1.outcome }}:tests/s1_outfile.out" \
+                       "Verification of stdlib update:${{ steps.pytest_2.outcome }}:tests/s2_outfile.out" \
+                       "Non-parallelisable C tests:${{ steps.pytest_3.outcome }}:tests/s3_outfile.out" \
+                       "Fortran tests:${{ steps.pytest_4.outcome }}:tests/s4_outfile.out" \
+                       "Non-parallelisable Fortran tests:${{ steps.pytest_5.outcome }}:tests/s5_outfile.out" \
+                       "Ndarray tests for C stdlib:${{ steps.pytest_6.outcome }}:tests/s6_outfile.out" 
+
+      shell: ${{ inputs.shell_cmd }}
+