migrated tags for tests and added missing raw files (#206)

- No changes or evaluation of existing tests
- Tags for including tests that require data is changed to
**[.with-data]** and **--with-data** for C++ and python respectively
- Minor update to docs
- Added missing files to the test data repo

python/tests/conftest.py

@@ -6,20 +6,20 @@ import pytest
 
 def pytest_addoption(parser):
     parser.addoption(
-        "--files", action="store_true", default=False, help="run slow tests"
+        "--with-data", action="store_true", default=False, help="Run tests that require additional data"
     )
 
 
 def pytest_configure(config):
-    config.addinivalue_line("markers", "files: mark test as needing image files to run")
+    config.addinivalue_line("markers", "withdata: mark test as needing image files to run")
 
 
 def pytest_collection_modifyitems(config, items):
-    if config.getoption("--files"):
+    if config.getoption("--with-data"):
         return
-    skip = pytest.mark.skip(reason="need --files option to run")
+    skip = pytest.mark.skip(reason="need --with-data option to run")
     for item in items:
-        if "files" in item.keywords:
+        if "withdata" in item.keywords:
             item.add_marker(skip)
 
 

python/tests/test_ClusterFile.py

@@ -9,7 +9,7 @@ import pickle
 from aare import ClusterFile
 from conftest import test_data_path
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_cluster_file(test_data_path): 
     """Test ClusterFile""" 
     f =  ClusterFile(test_data_path / "clust/single_frame_97_clustrers.clust") 
@@ -39,7 +39,7 @@ def test_cluster_file(test_data_path):
     for i in range(10):
         assert arr[i]['x'] == i+1
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_read_clusters_and_fill_histogram(test_data_path): 
     # Create the histogram
     n_bins = 100

python/tests/test_RawFile.py

@@ -2,7 +2,7 @@ import pytest
 from aare import RawFile
 import numpy as np
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_read_rawfile_with_roi(test_data_path):
 
    with RawFile(test_data_path / "raw/SingleChipROI/Data_master_0.json") as f:
@@ -11,7 +11,7 @@ def test_read_rawfile_with_roi(test_data_path):
     assert headers.size == 10100
     assert frames.shape == (10100, 256, 256)
     
-@pytest.mark.files
+@pytest.mark.withdata
 def test_read_rawfile_quad_eiger_and_compare_to_numpy(test_data_path): 
     
     d0 = test_data_path/'raw/eiger_quad_data/W13_vrpreampscan_m21C_300V_800eV_vthre2000_d0_f0_0.raw'
@@ -36,7 +36,7 @@ def test_read_rawfile_quad_eiger_and_compare_to_numpy(test_data_path):
     assert (image == image1).all()
 
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_read_rawfile_eiger_and_compare_to_numpy(test_data_path): 
     d0 = test_data_path/'raw/eiger/Lab6_20500eV_2deg_20240629_d0_f0_7.raw'
     d1 = test_data_path/'raw/eiger/Lab6_20500eV_2deg_20240629_d1_f0_7.raw'

python/tests/test_RawSubFile.py

@@ -3,7 +3,7 @@ import numpy as np
 from aare import RawSubFile, DetectorType
 
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_read_a_jungfrau_RawSubFile(test_data_path):
 
     # Starting with f1 there is now 7 frames left in the series of files
@@ -23,7 +23,7 @@ def test_read_a_jungfrau_RawSubFile(test_data_path):
     data = np.load(test_data_path / "raw/jungfrau/jungfrau_single_0.npy")
     assert np.all(data[3:] == frames)
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_iterate_over_a_jungfrau_RawSubFile(test_data_path):
 
     data = np.load(test_data_path / "raw/jungfrau/jungfrau_single_0.npy")

python/tests/test_jungfrau_dat_files.py

@@ -2,7 +2,7 @@ import pytest
 import numpy as np
 from aare import JungfrauDataFile
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_jfungfrau_dat_read_number_of_frames(test_data_path):
     with JungfrauDataFile(test_data_path / "dat/AldoJF500k_000000.dat") as dat_file:
         assert dat_file.total_frames == 24
@@ -14,7 +14,7 @@ def test_jfungfrau_dat_read_number_of_frames(test_data_path):
         assert dat_file.total_frames == 113
 
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_jfungfrau_dat_read_number_of_file(test_data_path):
     with JungfrauDataFile(test_data_path / "dat/AldoJF500k_000000.dat") as dat_file:
         assert dat_file.n_files == 4
@@ -26,7 +26,7 @@ def test_jfungfrau_dat_read_number_of_file(test_data_path):
         assert dat_file.n_files == 7
 
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_read_module(test_data_path):
     """
     Read all frames from the series of .dat files. Compare to canned data in npz format. 
@@ -50,7 +50,7 @@ def test_read_module(test_data_path):
     assert np.all(ref_header == header)
     assert np.all(ref_data == data)
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_read_half_module(test_data_path):
 
     # Read all frames from the .dat file
@@ -71,7 +71,7 @@ def test_read_half_module(test_data_path):
     assert np.all(ref_data == data)
 
 
-@pytest.mark.files
+@pytest.mark.withdata
 def test_read_single_chip(test_data_path):
 
     # Read all frames from the .dat file