Merge pull request #49 from VERITAS-Observatory/spectral-5sigma

Add functionality to plot spectra for significant bins in light curve

Author: GernotMaier

.github/workflows/flake8.yml

@@ -1,9 +1,8 @@
 ---
-## Super Linter GitHub Actions ##
-name: Lint Code Base
+name: CI-linting
 
-# Start the job on all push #
 on:
+  workflow_dispatch:
   pull_request:
     branches: [main]
     types: [opened, synchronize]
@@ -12,35 +11,80 @@ on:
       - main
 
 jobs:
-  build:
-    name: Lint Code Base
+
+  linting:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
 
     permissions:
       contents: read
       packages: read
       statuses: write
 
     steps:
-      - name: Checkout Code
+      - name: checkout
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+
+      - 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
+            echo "Non-ASCII characters found in documentation."
+            exit 1
+          fi
+
+      - name: install packages not included in super-linter
+        run: |
+          pip install validate-pyproject
+
+      - name: pyproject.toml
+        run: |
+          validate-pyproject pyproject.toml
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/cffconvert-github-action@2.0.0
+        with:
+          args: "--validate"
+
+      # Dependencies required to avoid errors
+      # reported by linters
+      - name: Install mamba dependencies
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          init-shell: bash
+
+      - name: Python dependencies
+        run: |
+          pip install -e '.[tests,dev,doc]'
+
+      - name: Pre-commit
+        run: |
+          pre-commit run --all-files
+
       - name: Lint Code Base
         uses: super-linter/super-linter@v7
         env:
           VALIDATE_ALL_CODEBASE: false
           VALIDATE_GITHUB_ACTIONS: true
           VALIDATE_YAML: true
-          VALIDATE_PYTHON_ISORT: true
-          VALIDATE_PYTHON_FLAKE8: true
-          VALIDATE_PYTHON_BLACK: true
           VALIDATE_MARKDOWN: true
+          VALIDATE_NATURAL_LANGUAGE: true
           VALIDATE_DOCKERFILE_HADOLINT: true
+          VALIDATE_BASH: true
           LINTER_RULES_PATH: ./
-          PYTHON_BLACK_CONFIG_FILE: pyproject.toml
-          PYTHON_ISORT_CONFIG_FILE: pyproject.toml
 
           DEFAULT_BRANCH: main
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/linter.yml

@@ -8,3 +8,5 @@ __pycache__/
 v2dl5.egg-info
 
 v2dl5/_version.py
+
+.vscode

.gitignore

@@ -1,15 +1,11 @@
+---
 repos:
   # https://pycqa.github.io/isort/docs/configuration/black_compatibility.html#integration-with-pre-commit
   - repo: https://github.com/pycqa/isort
     rev: 6.0.1
     hooks:
       - id: isort
         args: ["--profile", "black", "--filter-files"]
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
-    hooks:
-      - id: black
-        args: ["--line-length=100"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff
     rev: v0.11.4

.pre-commit-config.yaml

@@ -12,6 +12,8 @@ Allows to run analysis scripts for a given list of runs or for a cone search aro
 
 - source detection analysis including integral flux (or flux upper limits), reflection region model
 - spectral analysis, reflected region model
+- run-list generation
+- light-curve analysis and plotting
 
 ## Installation
 
@@ -28,17 +30,17 @@ conda activate v2dl5
 pip install -e .
 ```
 
-## V2DL5 Analysis
+## Analysis
 
 ### Run list generator
 
-The tool `runlist.py` allows to generate a list of runs for a given observation time and zenith angle.
+The tool `generate_run_list.py` allows to generate a list of runs for a given observation time and zenith angle.
 It generates a lot of printout which should be used to fine tune the run selection.
 
 Example:
 
 ```console
-python v2dl5/scripts/generate_runlist.py \
+python v2dl5/scripts/generate_run_list.py \
     --obs_table ../../../VTS/DL3/v490/dl3_pointlike_moderate2tel/obs-index.fits.gz \
     --config examples/run_selection.yml \
    --output_dir my_output_dir
@@ -68,7 +70,7 @@ python v2dl5/scripts/plot_binary_light_curves.py \
 
 ### Auxiliary data
 
-Auxiliary data is stored in v2dl5/data and available at run time. This includes:
+Auxiliary data is stored in v2dl5/data and available at runtime. This includes:
 
 #### Star catalogues
 

README.md

@@ -21,3 +21,4 @@ dependencies:
   - pytest-xdist
   - python
   - scipy
+  - uproot

environment.yml

@@ -11,11 +11,11 @@ fi
 
 light_curves()
 {
-    ANASUM_FILE="/data/$(basename $1)"
-    TIME_FILE="/time_data/$(basename $2)"
+    ANASUM_FILE="/data/$(basename "$1")"
+    TIME_FILE="/time_data/$(basename "$2")"
     podman run --platform linux/amd64 --rm -it -v "$(pwd)/:/workdir" \
-        -v "$(dirname $1):/data" \
-        -v "$(dirname $2):/time_data" \
+        -v "$(dirname "$1"):/data" \
+        -v "$(dirname "$2"):/time_data" \
         ghcr.io/veritas-observatory/eventdisplay_v4:main \
         /bin/bash -c \
         "cd /workdir/; root -l -q -b 'light_curve_analysis.C(\"$ANASUM_FILE\", \"$TIME_FILE\", $3, $4, $5)';"

eventdisplay_anasum/light_curve_analysis.sh

@@ -11,11 +11,11 @@ fi
 
 runlist_from_time_bins()
 {
-    ANASUM_FILE="/data/$(basename $1)"
-    TIME_FILE="/time_data/$(basename $2)"
+    ANASUM_FILE="/data/$(basename "$1")"
+    TIME_FILE="/time_data/$(basename "$2")"
     podman run --platform linux/amd64 --rm -it -v "$(pwd)/:/workdir" \
-        -v "$(dirname $1):/data" \
-        -v "$(dirname $2):/time_data" \
+        -v "$(dirname "$1"):/data" \
+        -v "$(dirname "$2"):/time_data" \
         ghcr.io/veritas-observatory/eventdisplay_v4:main \
         /bin/bash -c \
         "cd /workdir/; root -l -q -b 'runlist_from_time_bins.C(\"$ANASUM_FILE\", \"$TIME_FILE\", $3)';"