changed answering PR report

Author: martinkilbinger

pyproject.toml

@@ -9,7 +9,7 @@ authors = [
     { name = "Martin Kilbinger", email = "martin.kilbinger@cea.fr" }
 ]
 license = { "file" = "LICENSE" }
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
     "joblib>=0.13",
     "modopt>=1.2",

scripts/python/clear_ngmix_prev.py

@@ -112,9 +112,9 @@ def main():
                 else:
                     n_objects, n_hdus = (-1, -1)
 
-                # File info of new
+                # File info of prev
                 prev_out_dir = prev_dir / "output"
-                fits_files = list(ngmix_out_dir.glob("ngmix-*.fits"))
+                fits_files = list(prev_out_dir.glob("ngmix-*.fits"))
                 if fits_files:
                     for fits_file in fits_files:
                         n_objects_prev, n_hdus_prev = get_fits_info(fits_file)

scripts/python/distribute_tiles.py

@@ -1,4 +1,4 @@
-#!/arc/home/kilbinger/.conda/envs/shapepipe/bin/python3.10
+#!/usr/bin/env python
 """
 distribute_tiles.py
 
@@ -121,7 +121,7 @@ def build_process_command(tile_id, original_args):
         elif original_args[i] in ('--batch_num', '--batch_tot', '--batch_size', '--parallel_jobs'):
             i += 2
         elif original_args[i] in ('-n', '--dry_run'):
-            if original_args[i] in (0, 1):
+            if original_args[i] in ("0", "1"):
                 cmd.extend(["-n", original_args[i]])
             i += 2
         else:

src/shapepipe/canfar/canfar_monitor.py

@@ -1,6 +1,6 @@
 # canfar_monitor.py
 
-# Montiot job submitted with the canfar client
+# Montior job submitted with the canfar client
 
 import os
 import sys
@@ -127,7 +127,7 @@ def filter(self):
             df['time'] = '12:04:00'
         except Exception as e:
             estr = f": {e}" if self._params["verbose"] else ""
-            raise RunTimeError(
+            raise RuntimeError(
                 f"An error occurred while processing dates: {estr}"
             ) from e
 
@@ -185,7 +185,7 @@ def destroy(self, df, session):
         bulk = self._params["bulk"]
 
         if bulk == 2:
-            kind = self._get_kind()
+            kind = self.get_kind()
 
             if self._params["status"] != "all":
                 status = self._params["status"]
@@ -202,10 +202,6 @@ def destroy(self, df, session):
             except Exception as e:
                 if self._params.get("verbose"):
                     print(f"Failed to destroy jobs: {e}")
-            else:
-                print("Failed to destroy jobs")
-                # Optionally exit or return gracefully
-                return False
 
             print("Success")
             return
@@ -219,7 +215,7 @@ def destroy(self, df, session):
                 print(f"{len(ids)} sessions done")
             except Exception as e:
                 estr = f": {e}" if self._params["verbose"] else ""
-                print("failed{estr}")
+                print(f"failed{estr}")
 
         else:
             print("Loop destroy")
@@ -232,7 +228,7 @@ def destroy(self, df, session):
                     print(f"{result[session_id]} done")
                 except Exception as e:
                     estr = f": {e}" if self._params["verbose"] else ""
-                    print("failed{estr}")
+                    print(f"failed{estr}")
 
 
     def get_session(self):
@@ -244,7 +240,7 @@ def get_session(self):
         try:
             if not self._params["quiet"]:
                 print(
-                    f"Retreiving session info of kind={self._params['kind']},"
+                    f"Retrieving session info of kind={self._params['kind']},"
                     + f" status={self._params['status']}"
                 )
             kind = self.get_kind()

src/shapepipe/canfar/canfar_submit.py

@@ -112,7 +112,7 @@ def params_default(self):
             "parallel_jobs": "number of tiles to process in parallel per replica; default is {}",
             "jobs_per_session": (
                 "number of jobs (tiles) per session; if 0, create one session per job (default is {});"
-                + " Number of replicas is #FILE_IDs / JOBS_PER_SESSSION"
+                + " Number of replicas is #FILE_IDs / JOBS_PER_SESSION"
             ),
             "stats": "print stats of sessions/batches/replicas and exit",
         }
@@ -130,7 +130,6 @@ def update_params(self):
                 self._params["cores"] = self._params["parallel_jobs"]
             else:
                 self._params["cores"] = self._cores_default
-        pass
 
     def check_params(self):
 

src/shapepipe/modules/make_cat_package/make_cat.py

@@ -345,14 +345,15 @@ def _save_ngmix_data(self, ngmix_cat_path, moments=False):
         # (1) shape measurement failures (e.g. missing PSF): ok, continue
         # (2) previous processing errors, e.g. premature run of
         # merge_sep_cats_runner: raise error
-        if len(ngmix_n_epoch) / self._cat_size_target < 0.0:
-            ngmix_cat_file.close()
+        if len(ngmix_n_epoch) / self._cat_size_target < 0.1:
             err_msg = (
                 f"Merged shape catalogue {ngmix_cat_path} has very different"
                 + f" size ({len(ngmix_n_epoch)}) compared to target size"
                 + f" {self._cat_size_target})"
             )
-            return err_msg
+            self._w_log.info(err_msg)
+            #ngmix_cat_file.close()
+            #return err_msg
 
         ngmix_mom_fail = ngmix_cat_file.get_data()["moments_fail"]
 

src/shapepipe/modules/mask_package/mask.py

@@ -495,9 +495,7 @@ def find_stars(self, position, radius):
             result = Vizier.query_region(coord, radius=radius*units.arcmin, catalog=self._CDS_cat_ID)
             if len(result) == 0:
                 raise IndexError(
-                    "Vizier astroquer returned empty list at ",
-                    coord,
-                    radius
+                    f"Vizier astroquery returned empty list at {coord}, {radius}"
                 )
             self._CDS_stdout = result[0]
 

src/shapepipe/modules/uncompress_fits_package/uncompress_fits.py

@@ -72,9 +72,9 @@ def process(self):
                         value = header_fitsio[name]
                         comment = header_fitsio.get_comment(name)
 
-                    # Optional: fix invalid TFORMn
-                    if name.startswith('TFORM') and isinstance(value, str) and 'PE' in value:
-                        value = '625E'
+                        # Optional: fix invalid TFORMn
+                        if name.startswith('TFORM') and isinstance(value, str) and 'PE' in value:
+                            value = '625E'
 
                     header[name] = (value, comment)
 

src/shapepipe/utilities/summary.py

@@ -215,7 +215,7 @@ def check_special_one(module, path):
                 if m:
                     code = 8
                     msg = "WCS world2pix did not converge"
-                    return mgs, code
+                    return msg, code
 
             if module == "ngmix_runner":
                 m = re.search("finished", line)
@@ -232,8 +232,8 @@ def check_special_one(module, path):
 
     if module == "ngmix_runner" and not ngmix_finished:
         code = 6
-        mgs = "ngmix incomplete"
-        return mgs, code
+        msg = "ngmix incomplete"
+        return msg, code
 
 
     return None, None