Merge branch 'fix/move_retrieve_yml_with_slurm' into 'master'

copy retrieve_constant to slurm and leave latest copy in out-folder

See merge request detectors/pycalibration!378

xfel_calibrate/finalize.py

@@ -186,8 +186,8 @@ def make_timing_summary(run_path, joblist, request_time, submission_time):
                                            time_table=time_table.split('\n'))))
 
 
-def make_report(run_path, tmp_path, out_path, project, author, version,
-                report_to):
+def make_report(run_path: str, tmp_path: str, out_path: str, project: str,
+                author: str, version: str, report_to: str):
     """
     Create calibration report (pdf file)
 
@@ -201,12 +201,13 @@ def make_report(run_path, tmp_path, out_path, project, author, version,
     :param project: Project title
     :param author: Author of the notebook
     :param version: Version of the notebook
-    :param report_to: Name or path of the report file
+    :param report_to: report path tailed with report name
     """
     run_path = path.abspath(run_path)
     report_path, report_name = path.split(report_to)
-    if report_path != '':
-        out_path = report_path
+
+    if not report_path:
+        report_path = out_path
 
     try:
         check_call([sys.executable, "-m", "sphinx.cmd.quickstart",
@@ -299,16 +300,18 @@ def make_report(run_path, tmp_path, out_path, project, author, version,
     # finally call the make scripts
     chdir(run_path)
     try:
-        check_call(["make", f"SPHINXBUILD={sys.executable} -m sphinx", "latexpdf"])
+        check_call(["make", f"SPHINXBUILD={sys.executable} -m sphinx",
+                    "latexpdf"])
 
     except CalledProcessError:
         print("Failed to make pdf documentation")
-        print("Temp files will not be deleted and " +
-              "can be inspected at: {}".format(run_path))
+        print("Temp files will not be deleted and "
+              f"can be inspected at: {run_path}")
         return
-    print("Moving report to final location: {}".format(out_path))
-    makedirs(out_path, exist_ok=True)
-    copy('{}/_build/latex/{}.pdf'.format(run_path, report_name), out_path)
+
+    print(f"Moving report to final location: {report_path}")
+    makedirs(report_path, exist_ok=True)
+    copy(f'{run_path}/_build/latex/{report_name}.pdf', report_path)
 
     temp_dirs = glob(f'{tmp_path}/*/')
     # Remove folders with figures and sphinx files.
@@ -318,15 +321,15 @@ def make_report(run_path, tmp_path, out_path, project, author, version,
 
     # Archiving files in slurm_tmp
     if os.path.isfile(f'{out_path}/retrieved_constants.yml'):
-        move(f'{out_path}/retrieved_constants.yml',
+        copy(f'{out_path}/retrieved_constants.yml',
              f"{tmp_path}")
 
     # Moving temporary files to out-folder after successful execution
     # This helps in keeping elements needed for re-producibility.
     print(f"Moving temporary files to final location"
-          f": {out_path}/{os.path.basename(tmp_path)} with name: "
+          f": {report_path}/{os.path.basename(tmp_path)} with name: "
           f"slurm_out_{report_name}")
-    move(tmp_path, f"{out_path}/slurm_out_{report_name}")
+    move(tmp_path, f"{report_path}/slurm_out_{report_name}")
 
 
 def make_titlepage(sphinx_path, project, data_path, version):