Cleaning up dead code (#156)

This PR cleans up lots of dead code.

.github/workflows/black.yml

@@ -14,7 +14,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: '3.12'
           cache: 'pip'
           cache-dependency-path: setup.py
 

.github/workflows/continous_integration.yml

@@ -32,24 +32,34 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
           cache-dependency-path: setup.py
 
+      - uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+            ${{ runner.os }}-pip-
+
       - name: Install dependencies
         run: |
           sudo apt-get update
           sudo apt-get install -y ffmpeg
           python -m pip install --upgrade pip
-          pip install pytest pytest-runner pytest-rerunfailures coveralls freezegun
-          pip install -e .
+          pip install -e ".[test]"
 
       - name: Run tests
-        run: coverage run -m pytest -v -s
+        run:  |
+          export NUMBA_DISABLE_JIT=1
+          python -m coverage run -m pytest -v -s
 
       - name: Run Coveralls
         if: ${{ success() }}

.github/workflows/isort.yml

@@ -9,10 +9,10 @@ jobs:
   isort:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: '3.12'
           cache: 'pip'
           cache-dependency-path: setup.py
 

README.md

@@ -62,11 +62,12 @@ If you want the latest version, we recommend creating a clean environment:
 ```commandline
 conda create -n gwemopt python=3.11
 git clone [email protected]:skyportal/gwemopt.git
-pip install -e gwemopt
+cd gwemopt
+pip install -e .
 pre-commit install
 ```
 
-or if you just want the latest version on Github:
+or if you just want the latest version released on PyPI:
 
 ```commandline
 pip install gwemopt
@@ -80,7 +81,7 @@ conda install -c astropy astroquery
 conda install -c conda-forge voeventlib astropy-healpix python-ligo-lw ligo-segments ligo.skymap ffmpeg
 ```
 
-And then run `pip install -e gwemopt` again.
+And then run `pip install -e .` again.
 
 # Usage
 
@@ -91,3 +92,17 @@ gwemopt-run ....
 ```
 
 where ... corresponds to the various arguments. 
+
+# Tests
+
+To run the tests, you'll first need to install gwemopt with the testing dependencies:
+
+```commandline
+pip install -e ".[test]"
+```
+
+Then you can run the tests using:
+
+```commandline
+coverage run -m pytest -v -s
+```

gwemopt/catalogs/get.py

@@ -2,9 +2,7 @@
 
 import healpy as hp
 import numpy as np
-from astropy.table import Table
 from astroquery.vizier import Vizier
-from ligo.skymap import distance
 from ligo.skymap.bayestar import derasterize
 from scipy.stats import norm
 

gwemopt/catalogs/mangrove.py

@@ -1,5 +1,4 @@
 import subprocess
-from pathlib import Path
 
 import numpy as np
 import pandas as pd

gwemopt/catalogs/nedlvs.py

@@ -1,5 +1,4 @@
 import subprocess
-from pathlib import Path
 
 import numpy as np
 import pandas as pd

gwemopt/catalogs/twomrs.py

@@ -4,6 +4,7 @@
 from astropy import units as u
 from astropy.cosmology import WMAP9 as cosmo
 from astropy.io.misc.hdf5 import read_table_hdf5, write_table_hdf5
+from astropy.table import Table
 from astroquery.vizier import Vizier
 from scipy.special import gammaincinv
 

gwemopt/chipgaps/decam.py

@@ -18,15 +18,12 @@
 This module contains the DECamtile class, which is used to calculate decam chip gaps
 """
 
-from array import array
-
 import astropy
-import healpy as hp
 import numpy as np
 from astropy import units as u
 from astropy.coordinates import ICRS, SkyCoord
 from astropy.wcs import WCS
-from mocpy import MOC, mocpy
+from mocpy import MOC
 from tqdm import tqdm
 
 
@@ -176,7 +173,6 @@ def get_decam_ccds(ra, dec, save_footprint=False):
     #    ccd_prob = CCDProb(ra, dec)
     decam_tile = DECamtile(ra, dec)
     ccd_cents_ra = decam_tile.ccd_RA
-    ccd_cents_dec = decam_tile.ccd_Dec
     offsets = np.asarray(
         [
             decam_tile._wcs[ccd_id].calc_footprint(axes=decam_tile.ccd_size)
@@ -229,10 +225,7 @@ def get_decam_quadrant_moc(ra, dec, n_threads=None):
         stacked = np.stack((ccd_coords.ra.deg, ccd_coords.dec.deg), axis=1)
         result = stacked.reshape(-1, ccd_coords.ra.deg.shape[1])
         lon_lat_list = [row for row in result]
-        moc = sum(
-            MOC.from_polygons(lon_lat_list, max_depth=np.uint8(10), n_threads=n_threads)
-        )
-        mocs.append(moc)
+        mocs.append(sum(MOC.from_polygons(lon_lat_list, False, 10, n_threads)))
 
     return mocs
 

gwemopt/chipgaps/ztf.py

@@ -20,7 +20,6 @@
 """
 
 import astropy
-import healpy as hp
 import numpy as np
 from astropy import units as u
 from astropy.coordinates import ICRS, SkyCoord
@@ -290,9 +289,6 @@ def get_ztf_quadrant_moc(ra, dec, n_threads=None):
         stacked = np.stack((ccd_coords.ra.deg, ccd_coords.dec.deg), axis=1)
         result = stacked.reshape(-1, ccd_coords.ra.deg.shape[1])
         lon_lat_list = [row for row in result]
-        moc = sum(
-            MOC.from_polygons(lon_lat_list, max_depth=np.uint8(10), n_threads=n_threads)
-        )
-        mocs.append(moc)
+        mocs.append(sum(MOC.from_polygons(lon_lat_list, False, 10, n_threads)))
 
     return mocs

gwemopt/coverage.py

@@ -1,13 +1,11 @@
 import copy
 
-import ligo.segments as segments
 import numpy as np
 import regions
 from astropy import units as u
 from astropy.coordinates import SkyCoord, get_sun
 from astropy.time import Time
 from mocpy import MOC
-from tqdm import tqdm
 
 import gwemopt.plotting
 import gwemopt.scheduler
@@ -16,7 +14,6 @@
 from gwemopt.tiles import (
     balance_tiles,
     check_overlapping_tiles,
-    eject_tiles,
     optimize_max_tiles,
     order_by_observability,
     slice_galaxy_tiles,
@@ -60,7 +57,6 @@ def combine_coverage_structs(coverage_structs):
 
 
 def read_coverage(params, telescope, filename, moc_struct=None):
-    nside = params["nside"]
     config_struct = params["config"][telescope]
     schedule_table = read_schedule(filename)
 
@@ -69,7 +65,7 @@ def read_coverage(params, telescope, filename, moc_struct=None):
     coverage_struct["filters"] = []
     coverage_struct["moc"] = []
 
-    for ii, row in schedule_table.iterrows():
+    for _, row in schedule_table.iterrows():
         ra, dec = row["ra"], row["dec"]
         tobs = row["tobs"]
         limmag = row["limmag"]
@@ -139,10 +135,9 @@ def powerlaw(params, map_struct, tile_structs, previous_coverage_struct=None):
     map_struct_hold = copy.deepcopy(map_struct)
 
     coverage_structs = []
-    n_scope = 0
     full_prob_map = map_struct["skymap"]
 
-    for jj, telescope in enumerate(params["telescopes"]):
+    for telescope in params["telescopes"]:
         config_struct = params["config"][telescope]
         tile_struct = tile_structs[telescope]
 
@@ -167,7 +162,7 @@ def powerlaw(params, map_struct, tile_structs, previous_coverage_struct=None):
             params_hold = copy.copy(params)
             config_struct_hold = copy.copy(config_struct)
 
-            coverage_struct, tile_struct = gwemopt.scheduler.schedule_alternating(
+            coverage_struct, tile_struct = gwemopt.tiles.schedule_alternating(
                 params_hold,
                 config_struct_hold,
                 telescope,
@@ -196,24 +191,22 @@ def powerlaw(params, map_struct, tile_structs, previous_coverage_struct=None):
                     (
                         coverage_struct,
                         tile_struct,
-                    ) = gwemopt.scheduler.schedule_alternating(
+                    ) = gwemopt.tiles.schedule_alternating(
                         params_hold,
                         config_struct_hold,
                         telescope,
                         map_struct_hold,
                         tile_struct,
                         previous_coverage_struct,
                     )
-                    doReschedule, balanced_fields = balance_tiles(
-                        params_hold, tile_struct, coverage_struct
-                    )
+                    doReschedule, _ = balance_tiles(params_hold, coverage_struct)
 
                     if doReschedule:
                         config_struct_hold = copy.copy(config_struct)
                         (
                             coverage_struct,
                             tile_struct,
-                        ) = gwemopt.scheduler.schedule_alternating(
+                        ) = gwemopt.tiles.schedule_alternating(
                             params_hold,
                             config_struct_hold,
                             telescope,
@@ -334,9 +327,7 @@ def powerlaw(params, map_struct, tile_structs, previous_coverage_struct=None):
             if params["doBalanceExposure"]:
                 cnt, ntrials = 0, 10
                 while cnt < ntrials:
-                    doReschedule, balanced_fields = balance_tiles(
-                        params, tile_struct, coverage_struct
-                    )
+                    doReschedule, _ = balance_tiles(params, coverage_struct)
                     if doReschedule:
                         for key in params["unbalanced_tiles"]:
                             tile_struct[key]["prob"] = 0.0
@@ -351,7 +342,7 @@ def powerlaw(params, map_struct, tile_structs, previous_coverage_struct=None):
 
             if params["max_nb_tiles"] is not None:
                 tile_struct, doReschedule = slice_number_tiles(
-                    params, telescope, tile_struct, coverage_struct
+                    params, tile_struct, coverage_struct
                 )
                 if doReschedule:
                     coverage_struct = gwemopt.scheduler.scheduler(

gwemopt/efficiency.py

@@ -6,7 +6,6 @@
 import scipy.stats
 from astropy.coordinates import SkyCoord
 from astropy.time import Time
-from ligo.skymap import distance
 from scipy.interpolate import interp1d
 
 from gwemopt.io.export_efficiency import (
@@ -94,9 +93,7 @@ def compute_efficiency(params, map_struct, lightcurve_struct, coverage_struct):
         efficiency_struct["dists_inj"] = dists_inj
 
     if params["true_location"]:
-        det = compute_true_efficiency(
-            params, map_struct, lightcurve_struct, coverage_struct
-        )
+        det = compute_true_efficiency(params, lightcurve_struct, coverage_struct)
 
         lc_name = lightcurve_struct["name"]
         save_detection_nondetection(
@@ -108,10 +105,7 @@ def compute_efficiency(params, map_struct, lightcurve_struct, coverage_struct):
     return efficiency_struct
 
 
-def compute_true_efficiency(params, map_struct, lightcurve_struct, coverage_struct):
-    nside = params["nside"]
-    npix = hp.nside2npix(nside)
-    Ninj = params["Ninj"]
+def compute_true_efficiency(params, lightcurve_struct, coverage_struct):
     gpstime = params["gpstime"]
     mjd_inj = Time(gpstime, format="gps", scale="utc").mjd
 
@@ -133,9 +127,7 @@ def compute_true_efficiency(params, map_struct, lightcurve_struct, coverage_stru
         lightcurve_mag = lightcurve_struct[filt]
         idx = np.where(np.isfinite(lightcurve_mag))[0]
 
-        f = interp.interp1d(
-            lightcurve_t[idx], lightcurve_mag[idx], fill_value="extrapolate"
-        )
+        f = interp1d(lightcurve_t[idx], lightcurve_mag[idx], fill_value="extrapolate")
         lightcurve_mag_interp = f(mjd)
         dist_threshold = (10 ** (((mag - lightcurve_mag_interp) / 5.0) + 1.0)) / 1e6
 

gwemopt/io/schedule.py

@@ -60,7 +60,7 @@ def read_schedule(schedule_path):
     return schedule
 
 
-def export_schedule_xml(xmlfile, map_struct, coverage_struct, config_struct):
+def export_schedule_xml(xmlfile, coverage_struct, config_struct):
     what = What()
 
     table = Table(name="data", Description=["The datas of GWAlert"])
@@ -157,9 +157,8 @@ def export_schedule_xml(xmlfile, map_struct, coverage_struct, config_struct):
         data = coverage_struct["data"][ii, :]
 
         ra, dec = data[0], data[1]
-        observ_time, exposure_time, field_id, prob, airmass = (
+        observ_time, field_id, prob, airmass = (
             data[2],
-            data[4],
             data[5],
             data[6],
             data[7],
@@ -195,15 +194,14 @@ def export_schedule_xml(xmlfile, map_struct, coverage_struct, config_struct):
 
 
 def summary(params, map_struct, coverage_struct, catalog_struct=None):
-
     filts = list(set(coverage_struct["filters"]))
     for jj, telescope in enumerate(params["telescopes"]):
         schedulefile = params["outputDir"].joinpath(f"schedule_{telescope}.dat")
         schedulexmlfile = params["outputDir"].joinpath(f"schedule_{telescope}.xml")
 
         config_struct = params["config"][telescope]
 
-        export_schedule_xml(schedulexmlfile, map_struct, coverage_struct, config_struct)
+        export_schedule_xml(schedulexmlfile, coverage_struct, config_struct)
 
         if (params["tilesType"] == "hierarchical") or (params["tilesType"] == "greedy"):
             fields = np.zeros((params["Ntiles"][jj], len(filts) + 2))
@@ -294,7 +292,6 @@ def summary(params, map_struct, coverage_struct, catalog_struct=None):
         for tt in tts:
             mjds_floor = []
             mjds = []
-            ipixs = np.empty((0, 2))
             cum_prob = 0.0
             cum_area = 0.0