First test

.github/workflows/ci.yml

@@ -52,7 +52,7 @@ jobs:
           python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
 
       - name: 🧪 Run Tests
-        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+        run: pytest --color=yes -rP --cov --cov-report=xml --cov-report=term-missing
 
       # If something goes wrong with --pre tests, we can open an issue in the repo
       - name: 📝 Report --pre Failures

pyproject.toml

@@ -40,6 +40,7 @@ dependencies = [
     "torch-fourier-shell-correlation",
     "ttmask",
     "matplotlib",
+    "numpy<2.0",
     "mrcfile",
     "plotille",
     "rich",
@@ -51,7 +52,7 @@ dependencies = [
 # "extras" (e.g. for `pip install .[test]`)
 [project.optional-dependencies]
 # add dependencies used for testing here
-test = ["pytest", "pytest-cov"]
+test = ["pytest", "pytest-cov", "pooch"]
 # add anything else you like to have in your dev environment here
 dev = [
     "ipython",

src/ttfsc/_cli.py

@@ -74,6 +74,7 @@ def ttfsc_cli(
     rprint(f"Estimated resolution using {fsc_threshold} criterion in unmasked map: {estimated_resolution_angstrom:.2f} Å")
 
     fsc_values_masked = None
+    fsc_values_corrected = None
     if mask != Masking.none:
         from ._masking import calculate_masked_fsc
 
@@ -138,7 +139,7 @@ def ttfsc_cli(
                     rlnSpectralIndex=i,
                     rlnResolution=r,
                     rlnAngstromResolution=r,
-                    rlnFourierShellCorrelationCorrected=fsc_values_corrected[i] if correct_for_masking else nan,
+                    rlnFourierShellCorrelationCorrected=fsc_values_corrected[i] if fsc_values_corrected is not None else nan,
                     rlnFourierShellCorrelationUnmaskedMaps=f,
                     rlnFourierShellCorrelationMaskedMaps=fsc_values_masked[i] if fsc_values_masked is not None else nan,
                     rlnCorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps=fsc_values_randomized[i]

tests/test_ttfsc.py

@@ -1,2 +1,33 @@
-def test_something():
-    pass
+import pooch
+import pytest
+from typer.testing import CliRunner
+
+from ttfsc._cli import cli
+
+
+@pytest.fixture(scope="module")
+def halfmap1():
+    fname = pooch.retrieve(
+        "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-37579/other/emd_37579_half_map_1.map.gz",
+        known_hash="e1c62f4eb3615d2c29c5cae6de3c10951e5aa828dac2f6aa04b0838dc2b96b6f",
+    )
+    return fname
+
+
+@pytest.fixture(scope="module")
+def halfmap2():
+    fname = pooch.retrieve(
+        "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-37579/other/emd_37579_half_map_2.map.gz",
+        known_hash="c076ee990a91715900e081a92a0747078ed5ec4796d35614f0b41025e5c24212",
+    )
+    return fname
+
+
+runner = CliRunner()
+
+
+def test_app(halfmap1, halfmap2):
+    result = runner.invoke(cli, [halfmap1, halfmap2])
+    print(result.output)
+    assert result.exit_code == 0
+    assert "Estimated resolution using 0.143 criterion in unmasked map: 3.63 Å" in result.output