Merge pull request #27 from tee-ar-ex/architecture_modif_python

Architectures change for Python only library

.github/workflows/python-package.yml

@@ -27,7 +27,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest pytest-cov
+        python -m pip install flake8 pytest pytest-cov pytest-console-scripts
         python -m pip install .
     - name: Lint with flake8
       run: |
@@ -37,4 +37,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest trx_file_memmap/tests
+        pytest trx/tests; pytest scripts/tests

README.md

@@ -1,9 +1,23 @@
-# tractography_file_format
-Official repository to present specifications, showcase examples, discuss issues and keep track of everything.
-Currently host only two file format propositions, the TRX file format(as memmap vs zarr). Anyone is free to contribute.
+# tee-ar-ex
+Official repository to present the TRX (tee-ar-ex) python implementation, discuss issues and keep track of everything.
+Anyone is free to contribute (issues, code reviews, pull requests).
 
-The library and scripts can be installed locally by using:
+Due to the fast change in implementation and possibily specifications, we recommend using a virtual environement.
+
+The library can be installed locally by using:
+```
+export TRX_MINIMAL_INSTALL=1
+pip install -e .
+```
+If you want to use the scripts and the functions related to the Stateful
+Tractogram using the following commands:
 ```
 pip install packaging>=19.0
+pip install cython>=0.29.24
 pip install -e .
 ```
+If you want to switch from a minimal (w/o Dipy) to a full (with Dipy) install
+you may need to add this before the above commands.
+```
+export TRX_MINIMAL_INSTALL=0
+```

scripts/tests/test_workflows.py

@@ -1,17 +1,23 @@
 #! /usr/bin/env python3
 # -*- coding: utf-8 -*-
 
+import logging
 import os
 import tempfile
 
-from dipy.io.streamline import load_tractogram
+import pytest
 import numpy as np
 from numpy.testing import assert_equal, assert_array_equal
-
-from trx_file_memmap.trx_file_memmap import load
-from tractography_file_format.fetcher import (get_testing_files_dict,
+try:
+    from dipy.io.streamline import load_tractogram
+    dipy_available = True
+except ImportError:
+    dipy_available = False
+
+from trx.trx_file_memmap import load
+from trx.fetcher import (get_testing_files_dict,
                                               fetch_data, get_home)
-from tractography_file_format.workflows import (convert_dsi_studio,
+from trx.workflows import (convert_dsi_studio,
                                                 convert_tractogram)
 
 
@@ -21,16 +27,25 @@
 
 
 def test_help_option_convert_dsi(script_runner):
+    if not dipy_available:
+        pytest.skip('Dipy library is missing, cannot test scripts involving '
+                      'tck/trk/vtk.')
     ret = script_runner.run('tff_convert_dsi_studio.py', '--help')
     assert ret.success
 
 
 def test_help_option_convert(script_runner):
+    if not dipy_available:
+        pytest.skip('Dipy library is missing, cannot test scripts involving '
+                      'tck/trk/vtk.')
     ret = script_runner.run('tff_convert_tractogram.py', '--help')
     assert ret.success
 
 
 def test_execution_convert_dsi():
+    if not dipy_available:
+        pytest.skip('Dipy library is missing, cannot test scripts involving '
+                      'tck/trk/vtk.')
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_trk = os.path.join(get_home(), 'DSI',
                           'CC.trk.gz')
@@ -53,6 +68,9 @@ def test_execution_convert_dsi():
 
 
 def test_execution_convert_to_trx():
+    if not dipy_available:
+        pytest.skip('Dipy library is missing, cannot test scripts involving '
+                      'tck/trk/vtk.')
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_trk = os.path.join(get_home(), 'DSI',
                           'CC_fix.trk')
@@ -73,6 +91,9 @@ def test_execution_convert_to_trx():
 
 
 def test_execution_convert_from_trx():
+    if not dipy_available:
+        pytest.skip('Dipy library is missing, cannot test scripts involving '
+                      'tck/trk/vtk.')
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_trk = os.path.join(get_home(), 'DSI',
                           'CC_fix.trk')
@@ -101,6 +122,9 @@ def test_execution_convert_from_trx():
 
 
 def test_execution_convert_dtype_p16_o64():
+    if not dipy_available:
+        pytest.skip('Dipy library is missing, cannot test scripts involving '
+                      'tck/trk/vtk.')
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_trk = os.path.join(get_home(), 'DSI',
                           'CC_fix.trk')
@@ -113,6 +137,9 @@ def test_execution_convert_dtype_p16_o64():
 
 
 def test_execution_convert_dtype_p64_o32():
+    if not dipy_available:
+        pytest.skip('Dipy library is missing, cannot test scripts involving '
+                      'tck/trk/vtk.')
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_trk = os.path.join(get_home(), 'DSI',
                           'CC_fix.trk')

scripts/tff_convert_dsi_studio.py

@@ -18,7 +18,7 @@
 import argparse
 import os
 
-from tractography_file_format.workflows import convert_dsi_studio
+from trx.workflows import convert_dsi_studio
 
 
 def _build_arg_parser():

scripts/tff_convert_tractogram.py

@@ -11,7 +11,7 @@
 import argparse
 import os
 
-from tractography_file_format.workflows import convert_tractogram
+from trx.workflows import convert_tractogram
 
 
 def _build_arg_parser():

scripts/tff_simple_compare.py

@@ -9,7 +9,7 @@
 
 import argparse
 
-from tractography_file_format.workflows import tractogram_simple_compare
+from trx.workflows import tractogram_simple_compare
 
 
 def _build_arg_parser():

scripts/tff_verify_header_compatibility.py

@@ -9,7 +9,7 @@
 """
 
 import argparse
-from tractography_file_format.workflows import verify_header_compatibility
+from trx.workflows import verify_header_compatibility
 
 
 def _build_arg_parser():

scripts/tff_visualize_overlap.py

@@ -7,7 +7,7 @@
 
 import argparse
 
-from tractography_file_format.workflows import tractogram_visualize_overlap
+from trx.workflows import tractogram_visualize_overlap
 
 
 def _build_arg_parser():

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
-name = tractography_file_format
-url = https://github.com/frheault/tractography_file_format
+name = trx
+url = https://github.com/tee-ar-ex/trx-python
 classifiers =
     Development Status :: 3 - Alpha
     Environment :: Console
@@ -18,9 +18,7 @@ platforms = OS Independent
 
 [options]
 python_requires = >=3.7
-install_requires =
-    dipy
+install_requires = nibabel
 
 [options.extras_require]
-dev =
-    pytest
+dev = pytest

setup.py

@@ -1,13 +1,23 @@
 import glob
+import os
 
 from setuptools import setup, find_packages
 
-SCRIPTS = glob.glob("scripts/*.py")
-REQUIRES = ['fury@git+https://github.com/frheault/fury.git@5059a529#egg=fury',
-            'dipy@git+https://github.com/frheault/dipy.git@4e192c5c6#egg=dipy',
-            'gdown>=4.*']
+TRX_MINIMAL_INSTALL = os.environ.get('TRX_MINIMAL_INSTALL')
+TRX_MINIMAL_INSTALL = False if TRX_MINIMAL_INSTALL is None else \
+    int(TRX_MINIMAL_INSTALL)
 
-setup(name='tractography_file_format',
+if TRX_MINIMAL_INSTALL:
+    SCRIPTS = None
+    REQUIRES = ['numpy>=1.20.*', 'nibabel>=3.*', 'gdown>=4.*',
+                'pytest>=7.*', 'pytest-console-scripts>=0.*']
+else:
+    SCRIPTS = glob.glob("scripts/*.py")
+    REQUIRES = ['fury@git+https://github.com/frheault/fury.git@5059a529#egg=fury',
+                'dipy@git+https://github.com/frheault/dipy.git@4e192c5c6#egg=dipy',
+                'gdown>=4.*', 'pytest>=7.*', 'pytest-console-scripts>=0.*']
+
+setup(name='trx',
       packages=find_packages(),
       setup_requires=['packaging>=19.0'],
       install_requires=REQUIRES,