gammasimtools 0.16.0__tar.gz → 0.18.0__tar.gz

{gammasimtools-0.16.0 → gammasimtools-0.18.0}/.env_template

@@ -6,7 +6,7 @@ SIMTOOLS_DB_SERVER='cta-simpipe-protodb.zeuthen.desy.de' # MongoDB server
 SIMTOOLS_DB_API_USER=YOUR_USERNAME # username for MongoDB: ask the responsible person
 SIMTOOLS_DB_API_PW=YOUR_PASSWORD # Password for MongoDB: ask the responsible person
 SIMTOOLS_DB_API_AUTHENTICATION_DATABASE='admin'
-SIMTOOLS_DB_SIMULATION_MODEL='CTAO-Simulation-ModelParameters-v0-5-2'
+SIMTOOLS_DB_SIMULATION_MODEL='CTAO-Simulation-ModelParameters-v0-7-0'
 SIMTOOLS_SIMTEL_PATH='/workdir/sim_telarray'
 SIMTOOLS_USER_NAME='simtools-user'
 SIMTOOLS_USER_ORGANIZATION='CTAO'

gammasimtools-0.18.0/.github/copilot-instructions.md

@@ -0,0 +1,19 @@
+This is a python project in the context of Monte Carlo simulations and high-energy gamma-ray astronomy.
+
+## Guidelines
+
+- use always semantic versions for version strings.
+- do not start replies with "this is the final outcome", while it is obviously not.
+- do not add trivial comments to the code (e.g. '# Adding five' before calling add_five()). Minimize the number of comments added.
+- Use pathlib, not os.path
+- Use logging, not print
+- Use f-strings for formatting of log messages and other strings.
+- Avoid hardcoding file paths
+
+##  Tests
+
+- unit test files should be in the ./tests/unit_tests/ directory and the directory structure there should follow that of the python package.
+- for unit tests, do not use test classes but simple test functions.
+- when writing unit tests, take care of the indentation of the method and the correct formatting.
+- check conftest.py for the pytest configuration and common fixtures.
+- put import statements at the top of the file. Avoid duplications of import statements.

{gammasimtools-0.16.0 → gammasimtools-0.18.0}/.github/workflows/CI-docs.yml

@@ -7,6 +7,8 @@ on:
   pull_request:
     branches: [main]
     types: [opened, closed, synchronize]
+  release:
+    types: [published]
 
 jobs:
 
@@ -22,7 +24,7 @@ jobs:
         with:
           python-version: "3.12"
 
-      - name: Python dependencies
+      - name: Install dependencies
         run: |
           pip install '.[doc]'
 
@@ -78,12 +80,22 @@ jobs:
           fi
           touch docs/build/html/.nojekyll
 
-      - name: Deploy to github pages
-        # only run when PR is merged
-        if: github.event.pull_request.merged
+      - name: Deploy versioned doc on release
+        if: github.event_name == 'release'
         uses: JamesIves/github-pages-deploy-action@v4
         with:
-          TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          BRANCH: gh-pages
-          FOLDER: docs/build/html
-          CLEAN: true
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          folder: docs/build/html
+          target-folder: ${{ github.ref_name }}  # e.g., v0.7.0
+          clean: false
+
+      - name: Deploy dev docs on PR merge to main
+        if: (github.event_name == 'pull_request' && github.event.pull_request.merged == true) || github.event_name == 'workflow_dispatch'
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          folder: docs/build/html
+          target-folder: .
+          clean: false

{gammasimtools-0.16.0 → gammasimtools-0.18.0}/.github/workflows/CI-integrationtests.yml

@@ -54,7 +54,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        model_version: ['6.0.0', '5.0.0', '6.0.0,5.0.0']
+        model_version: ['6.0.0', '5.0.0', '6.0.0,6.1.0']
 
     defaults:
       run:
@@ -86,6 +86,7 @@ jobs:
           SIMTOOLS_DB_SIMULATION_MODEL=$(grep 'SIMTOOLS_DB_SIMULATION_MODEL=' .env_template | cut -d '=' -f2- | tr -d '"')
           SIMTOOLS_DB_SIMULATION_MODEL="${SIMTOOLS_DB_SIMULATION_MODEL//\'/}"
           echo "SIMTOOLS_DB_SIMULATION_MODEL=$SIMTOOLS_DB_SIMULATION_MODEL" >> "$GITHUB_ENV"
+          echo "Simulation model set to: $SIMTOOLS_DB_SIMULATION_MODEL"
 
       - name: Create environment file (local DB)
         if: github.event_name != 'schedule'
@@ -115,4 +116,5 @@ jobs:
         run: |
           source /workdir/env/bin/activate
           pip install --no-cache-dir -e '.[tests,dev,doc]'
-          pytest --model_version=${{ matrix.model_version }} --color=yes --durations=20 -n 4 --dist loadscope --no-cov tests/integration_tests/
+          pytest --model_version=${{ matrix.model_version }} --color=yes --durations=20 \
+           -n 4 --dist loadscope --retries 2 --retry-delay 5 --no-cov tests/integration_tests/

{gammasimtools-0.16.0 → gammasimtools-0.18.0}/.github/workflows/CI-linter.yml

@@ -34,17 +34,29 @@ jobs:
         with:
           python-version: "3.12"
 
-
       - name: Check for non-ASCII characters
         run: |
-          output=$(find . -type f \
-          \( -name "*.py" -o -name "*.rst" -o -name "*.yml" -o -name "*.toml" \) \
-          -exec perl -ne 'print if /[^[:ascii:]]/ && !/latin/i' {} \;)
-          if [ -n "$output" ]; then
+          found=0
+          while IFS= read -r file; do
+            matches=$(perl -ne 'print if /[^[:ascii:]]/ && !/latin/i' "$file")
+            if [ -n "$matches" ]; then
+              echo "File: $file"
+              echo "$matches"
+              found=1
+            fi
+          done < <(find . -type f \( -name "*.py" -o -name "*.rst" -o -name "*.yml" -o -name "*.toml" \))
+
+          if [ "$found" -eq 1 ]; then
             echo "Non-ASCII characters found in documentation."
             exit 1
           fi
 
+      - name: Lint Docker files
+        run: |
+          find ./docker -name "Dockerfile-*" -print0 | while IFS= read -r -d '' dockerfile; do
+            docker run --rm -i ghcr.io/hadolint/hadolint < "$dockerfile"
+          done
+
       - name: install packages not included in super-linter
         run: |
           pip install validate-pyproject
@@ -83,8 +95,6 @@ jobs:
         uses: super-linter/super-linter@v7
         env:
           VALIDATE_ALL_CODEBASE: false
-          # docker
-          VALIDATE_DOCKERFILE_HADOLINT: true
           # .env file
           VALIDATE_ENV: true
           # language

{gammasimtools-0.16.0 → gammasimtools-0.18.0}/.github/workflows/CI-unittests.yml

@@ -128,13 +128,22 @@ jobs:
           SIMTOOLS_DB_SIMULATION_MODEL: ${{ env.SIMTOOLS_DB_SIMULATION_MODEL }}
         run: |
           pytest --durations=10 --color=yes -n 4 --dist loadscope \
-            --cov=simtools --cov-report=xml
+            --cov=simtools --cov-report=xml --retries 2 --retry-delay 5
 
       # CTAO-DPPS-SonarQube
-      - uses: SonarSource/sonarqube-scan-action@v5.1.0
+      - uses: SonarSource/sonarqube-scan-action@v5.2.0
         if: contains(matrix.extra-args, 'codecov')
         env:
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        with:
+          args: >
+            -Dsonar.projectKey=gammasim_simtools_AY_ssha9WiFxsX-2oy_w
+            -Dsonar.host.url=https://sonar-cta-dpps.zeuthen.desy.de
+            -Dsonar.qualitygate.wait=true
+            -Dsonar.python.coverage.reportPaths=coverage.xml
+            -Dsonar.python.version=${{ matrix.python-version }}
+            -Dsonar.exclusions="**/docs/**,src/simtools/applications/*,**__init__.py"
+            -Dsonar.coverage.exclusions="**/tests/**"
 
       - name: Random order
         if: github.event_name == 'schedule' && contains(matrix.extra-args, 'random-order')
@@ -142,7 +151,21 @@ jobs:
         env:
           SIMTOOLS_DB_SIMULATION_MODEL: ${{ env.SIMTOOLS_DB_SIMULATION_MODEL }}
         run: |
-          pytest --color=yes -n 4 --dist loadscope --count 5 --random-order
+          pytest --color=yes -n 4 --dist loadscope --count 5 --random-order \
+           --retries 2 --retry-delay 5
+
+      - name: Configure Codecov
+        if: contains(matrix.extra-args, 'codecov')
+        run: |
+          cat > codecov.yml << 'EOF'
+          comment: off
+          coverage:
+            status:
+              project:
+                default:
+                  target: auto
+                  threshold: 0.1%
+          EOF
 
       - name: Upload coverage report to codecov
         uses: codecov/codecov-action@v5

{gammasimtools-0.16.0 → gammasimtools-0.18.0}/.github/workflows/build-simtools-production-image.yml

@@ -33,7 +33,6 @@ jobs:
       - name: Download corsika-simtel-package
         run: |
           wget --no-verbose ${{ env.CLOUD_URL }}/${{ secrets[format('CLOUD_SIMTEL_{0}', matrix.simtel_version)] }}/download -O corsika_simtelarray_${{ matrix.simtel_version }}.tar.gz
-          wget --no-verbose ${{ env.CLOUD_URL }}/${{ secrets.CLOUD_CORSIKA_OPT }}/download -O corsikaOptPatch.tar.gz  # might depend on CORSIKA version
 
       - name: Upload corsika-simtel-package
         uses: actions/upload-artifact@v4
@@ -41,7 +40,6 @@ jobs:
           name: corsika-simtelarray-package-${{ matrix.simtel_version }}
           path: |
             corsika_simtelarray_${{ matrix.simtel_version }}.tar.gz
-            corsikaOptPatch.tar.gz
           retention-days: 1
 
   build-corsika-simtelarray:
@@ -58,7 +56,6 @@ jobs:
           # - {build_opt: 'prod5', extra_def: ''}
           # - {build_opt: 'prod5-sc', extra_def: ''}
         version:
-          # - {simtel_version: '240205', corsika_version: '77500', bernlohr_version: '1.67'}
           - {simtel_version: '240927', corsika_version: '77550', bernlohr_version: '1.68', hadronic_model: 'qgs2'}
           - {simtel_version: '250304', corsika_version: '78000', bernlohr_version: '1.69', hadronic_model: 'qgs3'}
 
@@ -133,9 +130,11 @@ jobs:
       matrix:
         version:
           # list of avx instructions: 'avx2', 'avx512f', 'sse4', 'avx'
+          - {simtel_version: '240205', corsika_version: '77500', bernlohr_version: '1.67', hadronic_model: 'qgs2', avx_instruction: 'no_opt'}
           - {simtel_version: '240927', corsika_version: '77550', bernlohr_version: '1.68', hadronic_model: 'qgs2', avx_instruction: 'no_opt'}
           - {simtel_version: '240927', corsika_version: '77550', bernlohr_version: '1.68', hadronic_model: 'qgs2', avx_instruction: 'avx2'}
           - {simtel_version: '250304', corsika_version: '78000', bernlohr_version: '1.69', hadronic_model: 'qgs3', avx_instruction: 'no_opt'}
+          - {simtel_version: '250304', corsika_version: '78000', bernlohr_version: '1.69', hadronic_model: 'qgs3', avx_instruction: 'avx2'}
         production:
           # list of productions build options: 'prod6-sc', 'prod6-baseline', 'prod5', 'prod5-sc'
           - {build_opt: 'prod6-sc', extra_def: ''}
@@ -157,7 +156,6 @@ jobs:
       - name: Rename corsika-simtel-package files and set build branch
         run: |
           mv ./downloaded-artifacts/corsika_simtelarray_${{ matrix.version.simtel_version }}.tar.gz corsika_simtelarray.tar.gz
-          mv ./downloaded-artifacts/corsikaOptPatch.tar.gz corsikaOptPatch.tar.gz
           if [[ "${{ github.event_name }}" == 'pull_request' ]]; then
             echo "BUILD_BRANCH=${GITHUB_HEAD_REF}" >> "$GITHUB_ENV"
           else
@@ -199,6 +197,7 @@ jobs:
             CORSIKA_VERSION=${{ matrix.version.corsika_version }}
             BERNLOHR_VERSION=${{ matrix.version.bernlohr_version }}
             BUILD_BRANCH=${{ env.BUILD_BRANCH }}
+            GITLAB_TOKEN_CORSIKA_OPT_PATCHES=${{ secrets.CORSIKA_OPT_PATCHES_GITLAB }}
           push:
             ${{ github.event_name == 'release' || github.event.pull_request.merged == true || github.event_name == 'workflow_dispatch' }}
           file: ./docker/Dockerfile-prod-opt
@@ -218,9 +217,11 @@ jobs:
       matrix:
         version:
           # list of avx instructions: 'avx2', 'avx512f', 'sse4', 'avx'
+          - {simtel_version: '240205', corsika_version: '77500', bernlohr_version: '1.67', hadronic_model: 'qgs2', avx_instruction: 'no_opt'}
           - {simtel_version: '240927', corsika_version: '77550', bernlohr_version: '1.68', hadronic_model: 'qgs2', avx_instruction: 'no_opt'}
           - {simtel_version: '240927', corsika_version: '77550', bernlohr_version: '1.68', hadronic_model: 'qgs2', avx_instruction: 'avx2'}
           - {simtel_version: '250304', corsika_version: '78000', bernlohr_version: '1.69', hadronic_model: 'qgs3', avx_instruction: 'no_opt'}
+          - {simtel_version: '250304', corsika_version: '78000', bernlohr_version: '1.69', hadronic_model: 'qgs3', avx_instruction: 'avx2'}
         production:
           # list of productions build options: 'prod6-sc', 'prod6-baseline', 'prod5', 'prod5-sc'
           - {build_opt: 'prod6-sc', extra_def: ''}

{gammasimtools-0.16.0 → gammasimtools-0.18.0}/.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 repos:
 # Ruff
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.11.7
+  rev: v0.12.1
   hooks:
   - id: ruff
     args: ["--fix"]
@@ -29,6 +29,7 @@ repos:
   - id: end-of-file-fixer
   - id: check-added-large-files
     args: ['--maxkb=500']
+  - id: check-json
 # https://github.com/HunterMcGushion/docstr_coverage
 - repo: https://github.com/HunterMcGushion/docstr_coverage
   rev: v2.3.2  # most recent docstr-coverage release or commit sha
@@ -42,7 +43,7 @@ repos:
   - id: actionlint
 # https://pyproject-fmt.readthedocs.io/en/latest/
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: "v2.5.1"
+  rev: "v2.6.0"
   hooks:
   - id: pyproject-fmt
 # codespell
@@ -52,13 +53,13 @@ repos:
   - id: codespell
 # markdownlint
 - repo: https://github.com/igorshubovych/markdownlint-cli
-  rev: v0.44.0
+  rev: v0.45.0
   hooks:
   - id: markdownlint
     args: ["--disable", "MD041"]
 # yamllint
 - repo: https://github.com/adrienverge/yamllint.git
-  rev: v1.37.0
+  rev: v1.37.1
   hooks:
   - id: yamllint
     args:

{gammasimtools-0.16.0 → gammasimtools-0.18.0}/CHANGELOG.md

@@ -7,6 +7,86 @@ This changelog is generated using [Towncrier](https://towncrier.readthedocs.io/)
 
 <!-- towncrier release notes start -->
 
+## [v0.18.0](https://github.com/gammasim/simtools/tree/v0.18.0) - 2025-07-08
+
+### Bugfixes
+
+- Run documentation generation CI on release to obtain current version of docs. ([#1607](https://github.com/gammasim/simtools/pull/1607))
+- Fix authentication errors in script to setup a local mongoDB. ([#1610](https://github.com/gammasim/simtools/pull/1610))
+
+### Documentation
+
+- Reorganisation and improvement of the documentation in the GitHub pages. ([#1611](https://github.com/gammasim/simtools/pull/1611))
+
+### New Features
+
+- Use CTAO telescope names when writing out telescope list in reduced event data tables. ([#1616](https://github.com/gammasim/simtools/pull/1616))
+- Allow CORSIKA limits to use layouts defined in simulation models database. ([#1619](https://github.com/gammasim/simtools/pull/1619))
+- Add application / API to plot tabulated model parameters using default plotting configurations defined in model parameters schemas. ([#1628](https://github.com/gammasim/simtools/pull/1628))
+- Allow to use current prod6 simulations for reduced event data generation. ([#1631](https://github.com/gammasim/simtools/pull/1631))
+- Add common array elements ID. Add list with triggered common telescope IDs to reduced event data tables. ([#1637](https://github.com/gammasim/simtools/pull/1637))
+
+### Maintenance
+
+- Removed unused ‘critical’ log level. ([#1604](https://github.com/gammasim/simtools/pull/1604))
+- Add JSON checker to pre-commit linter. ([#1615](https://github.com/gammasim/simtools/pull/1615))
+- Update test files with proton simulations (simtel output) and add provenance information. ([#1617](https://github.com/gammasim/simtools/pull/1617))
+- Improve linter CI to print file containing non-ascii characters. ([#1620](https://github.com/gammasim/simtools/pull/1620))
+- Replace file lists `tests/resources/simtel_output_files.txt` used for testing by explicitly listing of files. ([#1629](https://github.com/gammasim/simtools/pull/1629))
+- Add default plotting configuration for tabular data. Introduce consistent lower-cases for keys in plotting configuration schema. ([#1635](https://github.com/gammasim/simtools/pull/1635))
+
+
+## [0.17.0](https://github.com/gammasim/simtools/tree/0.17.0) - 2025-06-10
+
+### Bugfixes
+
+- Fix data type of 'dsum_threshold' parameter. ([#1557](https://github.com/gammasim/simtools/pull/1557))
+- Add missing neutrons to eventio particle IDs. ([#1584](https://github.com/gammasim/simtools/pull/1584))
+- Fix suffix for sim_telarray output files: no correctly `simtel.zst` (was `.zst` only) ([#1588](https://github.com/gammasim/simtools/pull/1588))
+
+### Documentation
+
+- Change documentation theme to pydata and add version switcher. ([#1560](https://github.com/gammasim/simtools/pull/1560))
+- Update documentation on how to run jobs using HT Condor. ([#1563](https://github.com/gammasim/simtools/pull/1563))
+
+### New Features
+
+- Add pixel layout plotting. ([#1541](https://github.com/gammasim/simtools/pull/1541))
+- Enable docker-image generation for vector-optimized CORSIKA 7.8. ([#1550](https://github.com/gammasim/simtools/pull/1550))
+- Add the sequential option to simulations using multipipe. With this option the CORSIKA and sim_telarray instances run in sequential order as far as possible. This mode is useful particularly on the grid, where typically we request a single core per job. ([#1561](https://github.com/gammasim/simtools/pull/1561))
+- Add reading and conversion of primary_id from sim_telarray output. ([#1570](https://github.com/gammasim/simtools/pull/1570))
+- Update `simtools-generate-simtel-event-data` to use astropy tables. ([#1573](https://github.com/gammasim/simtools/pull/1573))
+- Generalize table reading and writing. Add application to merge tables. ([#1580](https://github.com/gammasim/simtools/pull/1580))
+- Write reduced event data file as part of the cleanup stage of the simtools-simulate-prod application. ([#1588](https://github.com/gammasim/simtools/pull/1588))
+- Use patches for optimized CORSIKA from gitlab repository instead of cloud download. ([#1589](https://github.com/gammasim/simtools/pull/1589))
+- New utility simtools-verify-simulation-model-production-tables to verify completeness of model parameter repository. ([#1592](https://github.com/gammasim/simtools/pull/1592))
+- Add custom copilot instructions to support AI used by developers. ([#1594](https://github.com/gammasim/simtools/pull/1594))
+- Add new application `simtools-submit-array-layouts` to submit new array-layouts definition and validate the telescopes listed. ([#1596](https://github.com/gammasim/simtools/pull/1596))
+- Improve layout plotting; adding plotting of background layout. Add plotting of all layouts. ([#1597](https://github.com/gammasim/simtools/pull/1597))
+- Improve printout for assertion error for testing. ([#1598](https://github.com/gammasim/simtools/pull/1598))
+- Add production version and build options to sim_telarrary metadata. ([#1601](https://github.com/gammasim/simtools/pull/1601))
+
+### Maintenance
+
+- Add unit tests to increase coverage in interpolation handler. ([#1504](https://github.com/gammasim/simtools/pull/1504))
+- Docker file improvements: linter application; bugfix in extra flags for optimized CORSIKA compilation. ([#1544](https://github.com/gammasim/simtools/pull/1544))
+- Include stdout and stderr in error message of integration test. ([#1555](https://github.com/gammasim/simtools/pull/1555))
+- Add pytest-retry package for 'flaky test'. ([#1558](https://github.com/gammasim/simtools/pull/1558))
+- Reduce number of log-messages (INFO) for uploaded model parameters to DB. ([#1559](https://github.com/gammasim/simtools/pull/1559))
+- Replace the "run_number_start" argument with "run_number_offset" (clearer) and re-introduce the "run_number" argument to allow specifying a run number (to which the offset is added). ([#1562](https://github.com/gammasim/simtools/pull/1562))
+- Use telescope position files for setup in illuminator application and set correct obs level. ([#1566](https://github.com/gammasim/simtools/pull/1566))
+- Improve the names of the various simulation output files. They now follow the current convention in current productions, they contain a bit more information (e.g., the model version where it wasn't there before), and they are more consistent with each other. ([#1568](https://github.com/gammasim/simtools/pull/1568))
+- Improved interface and interpolation routines to derive production configuration. This creates a pipeline for lookup table generation, production grid generation, creating a grid with limits, which is then further complemented by the production statistics per grid point. ([#1569](https://github.com/gammasim/simtools/pull/1569))
+- Fix unit test to run with astropy 7.1 (and earlier versions) (see #1574). ([#1575](https://github.com/gammasim/simtools/pull/1575))
+- Simplified Sonar setup by moving properties into GitHub workflow. ([#1578](https://github.com/gammasim/simtools/pull/1578))
+- Introduce simplified Codecov configuration. ([#1579](https://github.com/gammasim/simtools/pull/1579))
+- Copy the CORSIKA log in binary mode instead of text mode. ([#1582](https://github.com/gammasim/simtools/pull/1582))
+- Protect against non-unicode characters in CORSIKA log file. ([#1583](https://github.com/gammasim/simtools/pull/1583))
+- Remove obsolete code on submission systems in JobManager. ([#1586](https://github.com/gammasim/simtools/pull/1586))
+- Change dummy trigger thresholds to easier-to-spot values. ([#1591](https://github.com/gammasim/simtools/pull/1591))
+- Fix duplication of some sim_telarray test files in './tests/resources' and corresponding test fixtures. ([#1593](https://github.com/gammasim/simtools/pull/1593))
+
+
 ## [v0.16.0](https://github.com/gammasim/simtools/tree/v0.16.0) - 2025-05-05
 
 ### Documentation

{gammasimtools-0.16.0/src/gammasimtools.egg-info → gammasimtools-0.18.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gammasimtools
-Version: 0.16.0
+Version: 0.18.0
 Summary: Tools for the Simulation System of the CTA Observatory
 Author-email: simtools developers <simtools-developer@desy.de>
 License-Expression: BSD-3-Clause
@@ -22,6 +22,7 @@ Requires-Dist: boost-histogram
 Requires-Dist: ctao-dpps-cosmic-ray-spectra
 Requires-Dist: ctapipe
 Requires-Dist: eventio
+Requires-Dist: h5py
 Requires-Dist: jsonschema
 Requires-Dist: matplotlib
 Requires-Dist: numpy
@@ -39,8 +40,9 @@ Requires-Dist: ruff; extra == "dev"
 Provides-Extra: doc
 Requires-Dist: myst-parser; extra == "doc"
 Requires-Dist: numpydoc; extra == "doc"
+Requires-Dist: pydata-sphinx-theme; extra == "doc"
 Requires-Dist: sphinx; extra == "doc"
-Requires-Dist: sphinx-book-theme; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
 Requires-Dist: towncrier; extra == "doc"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
@@ -50,6 +52,7 @@ Requires-Dist: pytest-profiling; extra == "tests"
 Requires-Dist: pytest-random-order; extra == "tests"
 Requires-Dist: pytest-repeat; extra == "tests"
 Requires-Dist: pytest-requirements; extra == "tests"
+Requires-Dist: pytest-retry; extra == "tests"
 Requires-Dist: pytest-xdist; extra == "tests"
 Dynamic: license-file
 

{gammasimtools-0.16.0 → gammasimtools-0.18.0}/database_scripts/setup_local_db.sh

@@ -17,14 +17,14 @@ else
     exit 1
 fi
 
-echo "Create network $SIMTOOLS_NETWORK"
+echo "Creating network $SIMTOOLS_NETWORK"
 $CMD network create $SIMTOOLS_NETWORK
 
-echo "Data directory ./mongo-data"
+echo "Creating data directory ./mongo-data"
 mkdir -p "$(pwd)"/mongo-data
 chmod 755 "$(pwd)"/mongo-data
 
-# Start mongoDB
+echo "Starting MongoDB container..."
 $CMD run -d \
   --name $CONTAINER_NAME \
   --network $SIMTOOLS_NETWORK \
@@ -33,31 +33,25 @@ $CMD run -d \
   -e MONGO_INITDB_ROOT_PASSWORD=example \
   -p 27017:27017 \
   -v "$(pwd)"/mongo-data:/data/db \
-  mongo:latest
+  mongo:8.0.10
 
-echo "Waiting for MongoDB to start..."
-sleep 5
-# Loop until MongoDB is ready
+echo "Waiting for MongoDB to be fully ready and root user to be available..."
 RETRIES=30
-until $CMD exec $CONTAINER_NAME mongosh --eval "db.runCommand({ ping: 1 })" >/dev/null 2>&1 || [ $RETRIES -eq 0 ]; do
-  echo "Waiting for MongoDB to be ready... ($((RETRIES--)) retries left)"
+until $CMD exec $CONTAINER_NAME mongosh admin -u root -p example --eval "db.runCommand({ connectionStatus: 1 })" >/dev/null 2>&1 || [ $RETRIES -eq 0 ]; do
+  echo "Waiting for MongoDB to be ready and root authable... ($((RETRIES--)) retries left)"
   sleep 2
 done
 if [ $RETRIES -eq 0 ]; then
   echo "MongoDB did not start in time."
-  exit 1
-fi
-
-# Verify root authentication
-echo "Verifying root authentication..."
-if ! $CMD exec $CONTAINER_NAME mongosh admin -u root -p example --eval "db.runCommand({ connectionStatus: 1 })"; then
-  echo "Error: Root authentication failed."
   $CMD logs $CONTAINER_NAME
   exit 1
 fi
+echo "MongoDB is ready and root authentication is working."
 
-echo "Create admin user"
-$CMD exec -it $CONTAINER_NAME mongosh admin -u root -p example --eval "
+echo "Creating 'api' user..."
+# This command *requires* the root user to be able to authenticate and have userAdminAnyDatabase role.
+# If this fails, the root setup was indeed the problem.
+if ! $CMD exec $CONTAINER_NAME mongosh admin -u root -p example --eval "
 db.createUser({
   user: 'api',
   pwd: 'password',
@@ -67,4 +61,9 @@ db.createUser({
     { role: 'userAdminAnyDatabase', db: 'admin' },
   ]
 });
-"
+"; then
+  echo "Error: Failed to create 'api' user. Check root credentials or MongoDB logs."
+  $CMD logs $CONTAINER_NAME
+  exit 1
+fi
+echo "'api' user created successfully."

{gammasimtools-0.16.0 → gammasimtools-0.18.0}/docker/Dockerfile-dev

@@ -1,9 +1,21 @@
+# Dockerfile for simtools development.
+#
+# Based on the CORSIKA and sim_telarray image.
+# All dependencies for simtools are installed,
+# but not simtools itself. It is expected that
+# simtools is installed in an external directory
+# mounted in the container.
+#
+# hadolint global ignore=DL3007,DL3013,DL3041,SC1091
+# - DL3007, DL3041: ignore warnings about using latest
+# - DL3013: ignore warnings about installing non-specific versions with microdnf)
+# - SC1091: ignore warning about not being able to source the bashrc
 ARG BUILD_OPT="prod6-baseline"
 ARG HADRONIC_MODEL="qgs2"
 ARG SIMTEL_VERSION="240927"
 ARG CORSIKA_VERSION="77550"
 ARG BERNLOHR_VERSION="1.68"
-FROM ghcr.io/gammasim/simtools-corsika-sim-telarray-${SIMTEL_VERSION}-corsika-${CORSIKA_VERSION}-bernlohr-${BERNLOHR_VERSION}-${BUILD_OPT}-${HADRONIC_MODEL}
+FROM ghcr.io/gammasim/simtools-corsika-sim-telarray-${SIMTEL_VERSION}-corsika-${CORSIKA_VERSION}-bernlohr-${BERNLOHR_VERSION}-${BUILD_OPT}-${HADRONIC_MODEL}:latest
 WORKDIR /workdir
 ARG PYTHON_VERSION="3.12"
 
@@ -15,8 +27,8 @@ RUN microdnf update -y && microdnf install -y \
 RUN wget --quiet https://raw.githubusercontent.com/gammasim/simtools/main/pyproject.toml && \
     python${PYTHON_VERSION} -m venv env && \
     source env/bin/activate && \
-    pip install -U pip && \
-    pip install toml-to-requirements && \
+    pip install --no-cache-dir -U pip && \
+    pip install --no-cache-dir toml-to-requirements && \
     toml-to-req --toml-file pyproject.toml --optional-lists dev,doc,tests && \
     pip uninstall -y toml-to-requirements && \
     pip install --no-cache-dir -r requirements.txt