Add unit tests and run them in the CI action

.github/workflows/run_test.yml

@@ -0,0 +1,39 @@
+name: CI tests
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Prepare mamba installation
+      env:
+          PYTHON_VERSION: '3.10'
+      run: |
+          # setup correct python version
+          sed -i -e "s/- python=.*/- python=$PYTHON_VERSION/g" environment.yml
+
+    - name: Mamba setup
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: environment.yml
+        cache-downloads: true
+
+    - name: Install dependencies
+      run: |
+        python --version
+        echo "Installing additional pip packages"
+
+        echo "pip install ."
+        pip install .
+
+        pip install pytest
+
+    - name: Test with pytest
+      run: |
+        pytest

.gitignore

@@ -131,3 +131,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Ruff
+output_ruff.txt

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.8
+    hooks:
+      - id: ruff
+        name: ruff linting
+        args: ["--config=pyproject.toml"]
+      - id : ruff-format
+        name: ruff formatting
+        args: ["--config=pyproject.toml"]

environment.yml

@@ -42,6 +42,6 @@ dependencies:
   - zstandard
   - conda-forge::eventio>=1.9.1,<2.0.0a0
   - pip:
-      - lstchain~=0.10.6
+      - lstchain==0.10.6
       - pint-pulsar<=0.9.7
-      - more-itertools
+      - more-itertools==10.4.0

ptiming_ana/__init__.py

@@ -2,9 +2,9 @@
 from . import phaseogram
 from .version import __version__
 
-__all__=[
-	"cphase",
-	"phaseogram",
-        "__version__",
-	"spectral",
+__all__ = [
+    "cphase",
+    "phaseogram",
+    "__version__",
+    "spectral",
 ]

ptiming_ana/_dev_version/__init__.py

@@ -1,4 +1,4 @@
-#Try to use setuptools_scm to get the current version; this is only used
+# Try to use setuptools_scm to get the current version; this is only used
 # in development installations from the git repository.
 # see lstchain/version.py for details
 try:

ptiming_ana/_version.py

@@ -3,6 +3,7 @@
 TYPE_CHECKING = False
 if TYPE_CHECKING:
     from typing import Tuple, Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +13,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.3.dev127+g6d5e09f.d20240620'
-__version_tuple__ = version_tuple = (0, 3, 'dev127', 'g6d5e09f.d20240620')
+__version__ = version = "0.6.dev4+g14a7d6b.d20240830"
+__version_tuple__ = version_tuple = (0, 6, "dev4", "g14a7d6b.d20240830")

ptiming_ana/cphase/__init__.py

@@ -1,12 +1,13 @@
-from .utils import  add_mjd,dl2time_totim,merge_dl2_pulsar, model_fromephem
-from .pulsarphase_cal import DL2_calphase,DL3_calphase,fermi_calphase
+from .utils import add_mjd, dl2time_totim, merge_dl2_pulsar, model_fromephem
+from .pulsarphase_cal import DL2_calphase, DL3_calphase, fermi_calphase
 
 
-__all__=[
-        'dl2time_totim',
-        'model_fromephem',
-        'add_mjd',
-        'DL3_calphase',
-        'DL2_calphase',
-        'merge_dl2_pulsar',
-        ]
+__all__ = [
+    "dl2time_totim",
+    "model_fromephem",
+    "add_mjd",
+    "DL3_calphase",
+    "DL2_calphase",
+    "merge_dl2_pulsar",
+    "fermi_calphase",
+]

ptiming_ana/cphase/add_DL2_phase_table.py

@@ -1,16 +1,16 @@
 #####################
 ###Author: Alvaro Mas Aguilar (alvmas)
-#mail: [email protected]
-#Using modules from PINT-pulsar and lstchain to calculate phases and add them to the input files in a new table called phase_info
+# mail: [email protected]
+# Using modules from PINT-pulsar and lstchain to calculate phases and add them to the input files in a new table called phase_info
 ###################3
 
 
-'''
+"""
 Script that adds the information of the phases and corrected times for the pulsar analysis to a DL2 file. It includes this information in a new table called 'phase_info' and optionally a new table with the ource position and theta2 values (called 'source_position')
 
 Parameters:
 ----------------------
---dir: string 
+--dir: string
   Directory where to find the standard DL3 files
 
 --in-file: string
@@ -19,110 +19,168 @@
 --ephem:string
   Path to the ephemeris file (.par or .gro)
 
---run-number: int 
+--run-number: int
   Run number to process (only if --dir is given)
 
 --include-theta: boolean
   True if want to add the source position and theta2 values on the DL2 files (in a table called 'source_position')
 
---interpolation: boolean 
+--interpolation: boolean
   Set to True if want to use the interpolation method (faster but loses some precision)
-   
+
 --number-interpolation: int
   Number of events between two interpolation points.
 
 
 Usage:
 ------------------------
 1. An example of usage for a given file is:
-python add_DL2_phase_table.py 
-       --in-file ./DL2_directory/dl2_LST-1.Run0000.fits.gz 
+python add_DL2_phase_table.py
+       --in-file ./DL2_directory/dl2_LST-1.Run0000.fits.gz
        --ephem model_test.par
 
 2. Another way of calling (if we have a directory and the run number) is:
-python add_DL2_phase_table.py 
+python add_DL2_phase_table.py
        --dir ./DL2_directory/
        --run-number 0000
        --ephem model_test.par
 
 3. If we want to use the interpolation method:
-python add_DL2_phase_table.py 
-       --in_file ./DL2_directory/dl3_LST-1.Run0000.fits.gz 
+python add_DL2_phase_table.py
+       --in_file ./DL2_directory/dl3_LST-1.Run0000.fits.gz
        --ephem model_test.par
        --interpolation
 
 4. If we want to include the source position and the theta2 values:
-python add_DL2_phase_table.py 
-       --in_file ./DL2_directory/dl3_LST-1.Run0000.fits.gz 
+python add_DL2_phase_table.py
+       --in_file ./DL2_directory/dl3_LST-1.Run0000.fits.gz
        --ephem model_test.par
        --interpolation
        --include-theta
 
-'''
+"""
 
-import sys
 import pandas as pd
 import argparse
-import numpy as np
 import os
-import warnings
 from ptiming_ana.cphase.pulsarphase_cal import DL2_calphase
 from ptiming_ana.cphase.utils import add_source_info_dl2
 
+
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument('--dir', '-d', action='store',type=str,dest='directory',default=None,help = 'Directory where to find the standard DL3 files (one by one)')
-    parser.add_argument('--in-file', '-f', action='store',type=str,dest='in_file',default=None,help = 'DL3 file to process (if want to analyze only one file)')
-    parser.add_argument('--ephem','-ephem',action='store',type=str,dest='ephem',default=None, help = 'Path to the ephemeris file (.par or .gro)')
-    parser.add_argument('--pickle','-pickle',action='store',type=bool,dest='pickle',default=False, help ='True if pickle, False otherwise')
-    parser.add_argument('--run-number','-r',action='store',type=str,dest='run',default=False, help = 'Run number to process (only if --dir is given)' )
-    parser.add_argument('--include-theta','-t',action='store_true',dest='include_theta', help ='True if want to add the source position and theta2 values on the DL2 files (in a table called source_position)')
-    parser.add_argument('--interpolation','-interp',action='store_true',dest='interpolation',help='Set to True if want to use the interpolation method (faster but loses some precision)')
-    parser.add_argument('--number-interpolation','-ninterp',action='store',type=int,dest='ninterp',default=1000, help ='Number of events between two interpolation points' )
-
+    parser.add_argument(
+        "--dir",
+        "-d",
+        action="store",
+        type=str,
+        dest="directory",
+        default=None,
+        help="Directory where to find the standard DL3 files (one by one)",
+    )
+    parser.add_argument(
+        "--in-file",
+        "-f",
+        action="store",
+        type=str,
+        dest="in_file",
+        default=None,
+        help="DL3 file to process (if want to analyze only one file)",
+    )
+    parser.add_argument(
+        "--ephem",
+        "-ephem",
+        action="store",
+        type=str,
+        dest="ephem",
+        default=None,
+        help="Path to the ephemeris file (.par or .gro)",
+    )
+    parser.add_argument(
+        "--pickle",
+        "-pickle",
+        action="store",
+        type=bool,
+        dest="pickle",
+        default=False,
+        help="True if pickle, False otherwise",
+    )
+    parser.add_argument(
+        "--run-number",
+        "-r",
+        action="store",
+        type=str,
+        dest="run",
+        default=False,
+        help="Run number to process (only if --dir is given)",
+    )
+    parser.add_argument(
+        "--include-theta",
+        "-t",
+        action="store_true",
+        dest="include_theta",
+        help="True if want to add the source position and theta2 values on the DL2 files (in a table called source_position)",
+    )
+    parser.add_argument(
+        "--interpolation",
+        "-interp",
+        action="store_true",
+        dest="interpolation",
+        help="Set to True if want to use the interpolation method (faster but loses some precision)",
+    )
+    parser.add_argument(
+        "--number-interpolation",
+        "-ninterp",
+        action="store",
+        type=int,
+        dest="ninterp",
+        default=1000,
+        help="Number of events between two interpolation points",
+    )
+
     args = parser.parse_args()
 
-    ephem=args.ephem
-    pickle=args.pickle
-    in_file=args.in_file
-    run=args.run
-    include_theta=args.include_theta
-    interpolation=args.interpolation
-    ninterp=args.ninterp
-    dl2_params_lstcam_key='dl2/event/telescope/parameters/LST_LSTCam'
+    ephem = args.ephem
+    pickle = args.pickle
+    in_file = args.in_file
+    run = args.run
+    include_theta = args.include_theta
+    interpolation = args.interpolation
+    ninterp = args.ninterp
+
     pd.set_option("display.precision", 10)
     if ephem is None:
-      		raise ValueError('No ephemeris provided')
-                    
+        raise ValueError("No ephemeris provided")
+
     if args.directory is not None:
         if in_file is not None:
-            raise ValueError('Both directory and file were given, can only use one of them')
-
-        filelist=[]
+            raise ValueError(
+                "Both directory and file were given, can only use one of them"
+            )
+
+        filelist = []
         for x in os.listdir(args.directory):
             rel_dir = os.path.relpath(args.directory)
             rel_file = os.path.join(rel_dir, x)
             if run in rel_file:
                 filelist.append(rel_file)
-                
+
         filelist.sort()
-        for i in range(0,len(filelist)):
-            #Calculate the phases
-            DL2_calphase(filelist[i],ephem,'lst',interpolation,ninterp,pickle)
+        for i in range(0, len(filelist)):
+            # Calculate the phases
+            DL2_calphase(filelist[i], ephem, "lst", interpolation, ninterp, pickle)
             if include_theta:
-                add_source_info_dl2(filelist[i],'Crab')
-		
+                add_source_info_dl2(filelist[i], "Crab")
+
     else:
         if in_file is not None:
-            #Calculate the phases
-            DL2_calphase(in_file,ephem,'lst',interpolation,ninterp,pickle)
+            # Calculate the phases
+            DL2_calphase(in_file, ephem, "lst", interpolation, ninterp, pickle)
             if include_theta:
-                add_source_info_dl2(in_file,'Crab')
+                add_source_info_dl2(in_file, "Crab")
         else:
-            raise ValueError('No input file or directory given')
+            raise ValueError("No input file or directory given")
+
 
-
 if __name__ == "__main__":
     main()
-
-