refactor(repoe): resolve merge conflict

#46

.github/workflows/bump_version.yml

@@ -4,7 +4,8 @@ on:
   push:
     branches:
     # disabling it for now
-      - _main
+      - main
+      - *_rc
 
 jobs:
   bump_version:

CHANGELOG.md

@@ -1,31 +1,64 @@
-## Unreleased
-
-### Feat
-
-- **background_models**: adding a user defined smoothing sigma
+## 1.0.1 (2024-05-09)
 
 ### Fix
 
-- **gammapy_tools/analysis/rbm.py**: removing hard coded map size values
+- **pyproject.toml**: fixing versioning
+- **gammapy_tools/make_background/prepare_data.py**: adding overwrite option
 
 ### Refactor
 
-- **analysis_notebook**: updating example
-- **data_products**: removing plt.show
+- **gammapy_tools/__version__.py**: post test update
+- **__version__**: switching to __version__ for the version number
+
+## 1.0.0 (2024-05-07)
 
-## 0.1.3 (2024-02-07)
+### Feat
+
+- **utils/exclusion_finder.py**: adding exclusion finder
+- **gammapy_tools/fake_source_coordinates/process.py**: adding mimic_data
+- **make_background**: parallel reduction of background and mimic search
+- **gammapy_tools/make_background**: implementing a parallel + reduction method to spead up background generation
+- **make_background**: implementation of closed N background runs
+- **background_models**: adding a user defined smoothing sigma
 
 ### Fix
 
+- **pyproject.toml**: changing gammapy version
+- **gammapy_tools/make_background/background_models.py**: updating to gammapy1.2
+- **gammapy_tools/utils/exclusion_finder.py**: adding a check for gammacat and hawc
+- **gammapy_tools/utils/exclusion_finder.py**: correcting path
+- **gammapy_tools/utils/exclusion_finder.py**: correcting imports and file paths
+- **fake_source_coordinates/process.py**: adding safety check
+- **gammapy_tools/fake_source_coordinates/process.py**: fixing print and removing target
+- **process.py**: correcting background
+- **make_background**: storing kl_div table
+- **background_tools.py**: exposure searching
+- **prepare_data.py**: adding more info
+- **prepare_data.py**: raise error when no runs are found
+- **gammapy_tools/analysis/rbm.py**: removing hard coded map size values
+- **Hipparcos_MAG8_1997.dat**: updated hipparcos file to have correct colour column
 - **analysis**: update the analysis scripts to work with config files
 
 ### Refactor
 
+- **gammapy_tools/fake_source_coordinates/process.py**: adding more robust file finder
+- **fake_source_coordinates/process.py**: reincluding source when scrambling
+- **gammapy_tools/fake_source_coordinates/fake_location.py**: popping exisiting background
+- **make_background**: removing ignore warnings
+- **make_background.py**: removing additional background and allow previous method
+- **templates/config.py**: adding KL_DIV
+- **utils**: moving functions to utils
+- **analysis_notebook**: updating example
+- **data_products**: removing plt.show
 - **_version.**: bumping version
 - **analysis_notebook**: migrating analysis notebook
 - **fake_source_coordinates**: adding __all__
 - **pyproject.toml**: changing required to minimum python version
 
+### Perf
+
+- **gammapy_tools/utils/run_details.py**: Changed the mimic selection to perform a nested search
+
 ## 0.1.2 (2024-01-30)
 
 ### Fix

Dockerfile

@@ -1,7 +1,7 @@
 FROM jupyter/minimal-notebook AS base
 
 # Install gammapy
-RUN mamba install gcc jupyterlab --yes
+RUN mamba install gcc jupyterlab "gammapy==1.2" --yes
 WORKDIR /gammapy-tools
 
 
@@ -28,14 +28,17 @@ COPY --from=base /opt/conda /opt/conda
 WORKDIR /gammapy-tools/tmp_build
 
 # RUN gammapy download datasets
-ENV GAMMAPY_DATA=/gammapy-tools/gammapy-datasets/1.1/
+ENV GAMMAPY_DATA=/gammapy-tools/gammapy-datasets/1.2/
 RUN mkdir -p $GAMMAPY_DATA
+WORKDIR /gammapy-tools/
+RUN gammapy download datasets
 
 # Add package
 ADD --chown=1000:100 . /gammapy-tools/tmp_build/gammapy-tools
 WORKDIR /gammapy-tools/tmp_build/gammapy-tools
 
 
+
 # RUN ls -lah
 RUN pip install .
 # RUN ./gammapy_tools/Hipparcos_MAG8_1997.dat $GAMMAPY_DATA/catalogs/

docker-compose.yml

@@ -11,5 +11,5 @@ services:
       - JUPYTER_TOKEN=letmein
     volumes:
       # Replace with where your data is located
-      - /path/to/data:/local_data  
-      - $GAMMAPY_DATA:/gammapy-tools/gammapy-datasets/1.1/
+      - /home/obriens/DataAnalysis/Veritas/Gammapy:/local_data  
+      # - $GAMMAPY_DATA:/gammapy-tools/gammapy-datasets/1.1/

gammapy-tools.def

@@ -16,22 +16,27 @@ Stage: build
     # Port for jupyter lab
     export JPORT=8000
     export GAMMAPY_DATA=/gamma-tools/gammapy-datasets/1.2/
-    . "/opt/conda/etc/profile.d/conda.sh"
-    . /opt/conda/bin/activate 
-    export PATH=/opt/conda/bin/:$PATH
-
+    #. "/opt/conda/etc/profile.d/conda.sh"
+    #. /opt/conda/bin/activate 
+    #export PATH=/opt/conda/bin/:$PATH
+    . /opt/gammapy_tools/bin/activate
+
+
 %post
 
     apt update
     apt upgrade -y
-    apt install curl bash git gcc btop emacs -y
+    apt install curl bash git gcc btop emacs python3 python3-pip python3.12-venv -y
 
     # Install mamba and base env
-    curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
-    bash Miniforge3-$(uname)-$(uname -m).sh  -b -p /opt/conda
-    . /opt/conda/bin/activate 
-
-    mamba install -c conda-forge iminuit cmasher pip papermill matplotlib pip "jupyterlab==4.0.12"  notebook ipykernel ipython ipywidgets --yes 
+    #curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+    #bash Miniforge3-$(uname)-$(uname -m).sh  -b -p /opt/conda
+    #. /opt/conda/bin/activate 
+
+    python3 -m venv /opt/gammapy_tools
+    . /opt/gammapy_tools/bin/activate
+    pip install iminuit cmasher pip papermill matplotlib pip "jupyterlab==4.0.12"  notebook ipykernel ipython ipywidgets
+    #mamba install -c conda-forge iminuit cmasher pip papermill matplotlib pip "jupyterlab==4.0.12"  notebook ipykernel ipython ipywidgets --yes 
 
 
     # Install v2dl3
@@ -41,7 +46,7 @@ Stage: build
 
     # Because its an env install of requirements
     # Note the python version in the latest test throws issues with pytest
-    grep -A 100 "dependencies:" environment-eventdisplay.yml | grep "-" | grep -v "python" | awk '{print $2}' | xargs mamba install --yes
+    grep -A 100 "dependencies:" environment-eventdisplay.yml | grep "-" | grep -v "python" | awk '{print $2}' | xargs pip install
 
     # root_numpy throws issues too. Only VEGAS uses it
     mv setup.py _setup.py && grep -v "root_numpy" _setup.py > setup.py && pip install .
@@ -59,7 +64,7 @@ Stage: build
 
     cd /gamma-tools ; rm -r /gamma-tools/tmp_build
 
-    mamba clean -a --yes   
+    #mamba clean -a --yes   
     python -m pip cache purge
 
 

gammapy_tools/__init__.py

@@ -2,10 +2,12 @@
 from . import make_background
 from . import templates
 from . import fake_source_coordinates
-
+from .__version__ import __version__
 __all__ = (
     analysis.__all__
     + make_background.__all__
     + templates.__all__
     + fake_source_coordinates.__all__
+    + ["__version__"]
 )
+

gammapy_tools/analysis/data_products_LOCAL_4133777.py

@@ -1,4 +1,3 @@
-from pathlib import Path
 import numpy as np
 import astropy.units as u
 from astropy.coordinates import Angle, SkyCoord
@@ -11,7 +10,6 @@
 
 # %matplotlib inline
 import matplotlib.pyplot as plt
-from IPython.display import display
 
 # gammapy imports
 from gammapy.data import DataStore
@@ -35,10 +33,9 @@
     SkyModel,
 )
 from gammapy.estimators import LightCurveEstimator
-from gammapy.analysis import Analysis, AnalysisConfig
-from gammapy.catalog import SourceCatalogGammaCat, SourceCatalog3HWC
 from gammapy.visualization import plot_spectrum_datasets_off_regions
 
+
 def make_spectrum_RE(config, plot=True, return_stacked=False):
     """Make a RE spectrum
 
@@ -67,8 +64,12 @@ def make_spectrum_RE(config, plot=True, return_stacked=False):
     observations = datastore.get_observations()
 
     if config["run_selection"]["pos_from_DL3"]:  # get position from DL3 header
-        hdul = fits.open(config["io"]["out_dir"]+os.listdir(config["io"]["out_dir"])[0])
-        source_pos = SkyCoord(hdul[1].header["RA_OBJ"]*u.deg, hdul[1].header["DEC_OBJ"]*u.deg)
+        hdul = fits.open(
+            config["io"]["out_dir"] + os.listdir(config["io"]["out_dir"])[0]
+        )
+        source_pos = SkyCoord(
+            hdul[1].header["RA_OBJ"] * u.deg, hdul[1].header["DEC_OBJ"] * u.deg
+        )
     else:  # get position from ra/dec [deg]
         source_pos = SkyCoord(
             config["run_selection"]["source_ra"],
@@ -148,7 +149,9 @@ def make_spectrum_RE(config, plot=True, return_stacked=False):
         < 2.0
     )
     # star_mask &= (star_cat["mag"] + star_cat["colour"]) < 8
-    star_mask &= (star_cat["mag"]+star_cat["colour"])< config["sky_map"]["min_star_brightness"]
+    star_mask &= (star_cat["mag"] + star_cat["colour"]) < config["sky_map"][
+        "min_star_brightness"
+    ]
 
     for src in star_cat[star_mask]:
         exclusion_regions.append(
@@ -192,13 +195,15 @@ def make_spectrum_RE(config, plot=True, return_stacked=False):
     info_table = datasets.info_table(cumulative=True)
     time = info_table["livetime"].to("h")
     sig = info_table["sqrt_ts"]
-    
-    #plot exclusion regions and reflected regions
-    if len(exclusion_regions) >  0 and plot:
-        plt.figure(figsize=(8,8))
+
+    # plot exclusion regions and reflected regions
+    if len(exclusion_regions) > 0 and plot:
+        plt.figure(figsize=(8, 8))
         ax = exclusion_mask.plot()
-        on_region.to_pixel(ax.wcs).plot(ax=ax, edgecolor="magenta",label='ON')
-        plot_spectrum_datasets_off_regions(ax=ax, datasets=datasets) #add legend=True to plot run numbers associated w/ OFF regions
+        on_region.to_pixel(ax.wcs).plot(ax=ax, edgecolor="magenta", label="ON")
+        plot_spectrum_datasets_off_regions(
+            ax=ax, datasets=datasets
+        )  # add legend=True to plot run numbers associated w/ OFF regions
         plt.show()
 
     # make spectrum model from user input
@@ -272,25 +277,32 @@ def get_flux_lc(config, type="flux"):
 
     theta = config["sky_map"]["theta"]
     datastore = DataStore.from_dir(config["io"]["out_dir"])
-    
+
     if config["io"]["from_runlist"]:
-        observations = datastore.get_observations(obs_id=np.genfromtxt(config["io"]["runlist"],unpack=True),required_irf="all-optional")
+        observations = datastore.get_observations(
+            obs_id=np.genfromtxt(config["io"]["runlist"], unpack=True),
+            required_irf="all-optional",
+        )
     else:
         observations = datastore.get_observations(required_irf="all-optional")
-    
+
     amp, idx = config["spectrum"]["params"]
-    
+
     if config["run_selection"]["pos_from_DL3"]:  # get position from DL3 header
-        hdul = fits.open(config["io"]["out_dir"]+os.listdir(config["io"]["out_dir"])[0])
-        source_pos = SkyCoord(hdul[1].header["RA_OBJ"]*u.deg, hdul[1].header["DEC_OBJ"]*u.deg)
+        hdul = fits.open(
+            config["io"]["out_dir"] + os.listdir(config["io"]["out_dir"])[0]
+        )
+        source_pos = SkyCoord(
+            hdul[1].header["RA_OBJ"] * u.deg, hdul[1].header["DEC_OBJ"] * u.deg
+        )
     else:  # get position from ra/dec [deg]
         source_pos = SkyCoord(
             config["run_selection"]["source_ra"],
             config["run_selection"]["source_dec"],
             frame="icrs",
             unit="deg",
         )
-    
+
     e_min = config["spectrum"]["e_min"]
     e_max = config["spectrum"]["e_max"]
     nbin = config["spectrum"]["e_bins"]
@@ -315,13 +327,13 @@ def get_flux_lc(config, type="flux"):
 
     # exclusion regions
     exclusion_regions = []
-    
+
     exclusion_regions.append(
         CircleSkyRegion(
             center=source_pos, radius=config["sky_map"]["on_exclusion_region"] * u.deg
         )
     )
-    
+
     if (
         len(config["sky_map"]["exclusion_regions"]) > 0
     ):  # should be a list of CircleSkyRegions
@@ -358,7 +370,7 @@ def get_flux_lc(config, type="flux"):
             "dec": star_data[:, 1],
             "id": star_data[:, 2],
             "mag": star_data[:, 3],
-            "colour": star_data[:,4],
+            "colour": star_data[:, 4],
         }
     )
     star_mask = (
@@ -369,8 +381,10 @@ def get_flux_lc(config, type="flux"):
         < 2.0
     )
 
-    star_mask &= (star_cat["mag"]+star_cat["colour"])< config["sky_map"]["min_star_brightness"]
-
+    star_mask &= (star_cat["mag"] + star_cat["colour"]) < config["sky_map"][
+        "min_star_brightness"
+    ]
+
     for src in star_cat[star_mask]:
         exclusion_regions.append(
             CircleSkyRegion(
@@ -404,7 +418,7 @@ def get_flux_lc(config, type="flux"):
     if type == "flux":
         time_intervals = [Time([start, stop])]
         lc_maker_1d = LightCurveEstimator(
-            energy_edges=[e_min,e_max] * u.TeV,
+            energy_edges=[e_min, e_max] * u.TeV,
             time_intervals=time_intervals,
             n_sigma_ul=2,
             reoptimize=False,