fixed test suite

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+filterwarnings =
+    ignore::UserWarning

src/cristallina/analysis.py

@@ -13,6 +13,9 @@ from joblib import Parallel, delayed, Memory
 from . import utils
 from .utils import ROI
 
+# Ideally we automatically determine the cache directory tied to the p-group
+# If this fails we try with a fixed path for now, and finally use the 
+# current temporary directory.
 try:
     pgroup = utils.heuristic_extract_pgroup()
     location = f"/das/work/units/cristallina/p{pgroup}/cachedir"
@@ -20,7 +23,12 @@ except KeyError as e:
     print(e)
     location = "/das/work/units/cristallina/p19739/cachedir"
 
-memory = Memory(location, verbose=0, compress=2)
+try:
+    memory = Memory(location, verbose=0, compress=2)
+except PermissionError as e:
+    location = "/tmp"
+    memory = Memory(location, verbose=0, compress=2)
+    
 
 
 @memory.cache(ignore=["batch_size"])  # we ignore batch_size for caching purposes

src/cristallina/utils.py

@@ -8,7 +8,7 @@ from sfdata import SFDataFiles, sfdatafile, SFScanInfo, SFProcFile
 from xraydb import material_mu
 from joblib import Parallel, delayed, cpu_count
 
-def scan_info(run_number,base_path=None,small_data=True):
+def scan_info(run_number, base_path=None, small_data=True):
     """Returns SFScanInfo object for a given run number. 
     If there is are small data channels, they will be added (small_data=False to suppress their loading).
     """
@@ -45,10 +45,7 @@ def print_run_info(
 
     Extra verbose output contains all files and pids.
     """
-    # if base_path == None:
-    # 	base_path = heuristic_extract_base_path()
-    # scan = SFScanInfo(f"{base_path}/run{run_number:04}/meta/scan.json")
-    scan = scan_info(run_number,base_path=base_path)
+    scan = scan_info(run_number, base_path=base_path)
     short = {}
     for key, value in scan.info.items():
         if isinstance(value, list):

tests/test_utils.py

@@ -6,7 +6,10 @@ from cristallina.utils import ROI, print_run_info, heuristic_extract_pgroup, gau
 __author__ = "Alexander Steppke"
 
 def test_print(capsys):
+    # this currently works only if the heuristic p-group extraction works
+    # TODO: fix this shortcoming and use base_path throughout
 
+    os.chdir("/sf/cristallina/data/p19739/")
     print_run_info(247)
     captured = capsys.readouterr()
     assert "15453208940" in captured.out