Issue/92/orbfit improvement (#95)

* new script to manage the files read and write by orbfit

* import the file management function in orbfit_local and orbfit_merger

* fix some bugs and finish integration of the new orbfit file management

* pep8 requirements

* finish to rewrite the orbfit system

* update doc

* pep8 requirements

* fix ephem bug

* fix test buggy paste

* fix test in orbfit_files.py

* new test for orbfit_files.py

* add new options to orbfit local

* pep8 requirements

* remove read_oel from orbfit_merger

* add K21E00A_test.oel

* pep8 requirements

* fix bug in the mpc obs file writer

* add a lot of test for the mpc obs writer

* add verbose level of orbfit

* fix verbose orbfit

* fix verbose orbfit

* some improvements

* fix ram_dir bug

* add more test, the trajectory merger with OrbFit works again

* update licence

* remove the old ephem.py, add the orbfit_ephem.py

* add test for the orbfit merger

* update test

* pep8 requirements

* update pickle version for test

* install pickle5

* update oop file generator, step_ephem is now an option and will not be write in the file if not set

* add an option to skip the initial orbit fitting if a .oel file exist

* fix test bug

* fix test bug

* restore test

* add an options to the write_oop, we can now specify the path of a .oel file

* update test

* update cli merge orbit

* bump to 0.8.0

.flake8

@@ -11,10 +11,13 @@ exclude =
     dist
     fink_fat/others/plot_perf_test.py
     fink_fat/others/night_report.py
+    ../fink-fat/fink_fat_out_2/mpc/test_assoc_tag.py
 count
 show-source
 statistics
 per-file-ignores =
+    ../fink-fat/fink_fat/orbit_fitting/orbfit_files.py:W503
+    ../fink-fat/fink_fat/orbit_fitting/mpcobs_files.py:W503
     ../fink-fat/fink_fat/orbit_fitting/orbfit_local.py:W503
     ../fink-fat/fink_fat/orbit_fitting/orbfit_cluster.py:W503
     ../fink-fat/fink_fat/orbit_fitting/orbfit_merger.py:W503

.github/workflows/run_test.yml

@@ -31,6 +31,9 @@ jobs:
         - name: install OrbFit SoftWare
           run: |
             ./fink_fat/test/orbFit_installer.sh
+        - name: update pickle
+          run: |
+            pip install pickle5
         - name: Run test suites
           run: |
             ./run_test.sh

LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright [yyyy] [name of copyright owner]
+   Copyright [2022] [Le Montagner Roman]
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

bin/fink_fat_cli.py

@@ -50,6 +50,7 @@
 import datetime
 import glob
 from astropy import units as u
+from astropy.time import Time
 from terminaltables import DoubleTable, AsciiTable, SingleTable
 from bin.offline_cli import offline_intro_reset, offline_yes_reset
 from bin.orbit_cli import (
@@ -72,7 +73,7 @@
 from fink_fat.associations.inter_night_associations import night_to_night_association
 from fink_fat.others.utils import cast_obs_data
 from fink_fat.orbit_fitting.orbfit_local import compute_df_orbit_param
-from fink_fat.orbit_fitting.orbfit_merger import orbit_identification
+from fink_fat.orbit_fitting.orbfit_merger import merge_orbit
 from bin.association_cli import (
     get_data,
     get_last_sso_alert,
@@ -346,16 +347,16 @@ def main():
 
             t_before = t.time()
             # call the orbit identification that will merge trajectories
-            merge_traj_orb, merger_orb_df = orbit_identification(
+            merge_traj = merge_orbit(
                 traj_orb_df,
                 orb_df,
                 config["SOLVE_ORBIT_PARAMS"]["ram_dir"],
                 int(config["MERGE_ORBIT_PARAMS"]["neighbor"]),
                 int(config["SOLVE_ORBIT_PARAMS"]["cpu_count"]),
+                prop_epoch=(Time.now() + 2 * u.hour).jd
             )
 
-            merge_traj_orb.to_parquet(traj_orb_path)
-            merger_orb_df.to_parquet(orb_res_path)
+            merge_traj.to_parquet(os.path.join(output_path, "merge_traj.parquet"))
 
             if arguments["--verbose"]:
                 print("Merging of the trajectories done !")

fink_fat/__init__.py

@@ -12,4 +12,4 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-__version__ = "0.7.1"
+__version__ = "0.8.0"