Merge pull request #167 from benjeffery/preprocess

Move preprocessing to separate step

README.md

@@ -8,13 +8,19 @@ It is particularly useful to help evaluate ARGs that have been inferred using to
 [KwARG](https://github.com/a-ignatieva/kwarg),
 [Threads](https://pypi.org/project/threads-arg/), etc.
 
+To view a tskit tree sequence or tszip file first pre-process it:
+
+`python -m tsbrowse preprocess /path/to/trees-file`
+
+This will write a `.tsbrowse` file
+
 To launch the app use:
 
-`python -m tsbrowse /path/to/trees-file`
+`python -m tsbrowse serve /path/to/tsbrowse-file`
 
 On WSL, it may be necessary to disable Numba's CUDA support:
 
-`NUMBA_DISABLE_CUDA=1 python -m tsbrowse /path/to/trees-file`
+`NUMBA_DISABLE_CUDA=1 python -m tsbrowse serve /path/to/tsbrowse-file`
 
 ## Installation
 

tests/test_cli.py

@@ -0,0 +1,31 @@
+import os
+
+import tszip
+from click.testing import CliRunner
+
+from . import test_preprocess
+from tsbrowse import __main__ as main
+
+
+def test_preprocess_cli(tmpdir):
+    tszip_path = os.path.join(tmpdir, "test_input.tszip")
+    default_output_path = os.path.join(tmpdir, "test_input.tsbrowse")
+    custom_output_path = os.path.join(tmpdir, "custom_input.tsbrowse")
+
+    ts = test_preprocess.single_tree_example_ts()
+    tszip.compress(ts, tszip_path)
+
+    runner = CliRunner()
+    result = runner.invoke(main.cli, ["preprocess", tszip_path])
+    assert result.exit_code == 0
+    assert os.path.exists(default_output_path)
+    tszip.load(default_output_path).tables.assert_equals(ts.tables)
+
+    result = runner.invoke(
+        main.cli, ["preprocess", tszip_path, "--output", custom_output_path]
+    )
+    assert result.exit_code == 0
+    assert os.path.exists(custom_output_path)
+    tszip.load(custom_output_path).tables.assert_equals(ts.tables)
+
+    # TODO Load into model and check that the model is correct