[REFAC] allowing the project to be installed as a python package

Inria-Empenn · Jan 24, 2023 · 1af1073 · 1af1073
1 parent 12183d4
commit 1af1073
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Showing 34 changed files with 52 additions and 7 deletions.
diff --git a/static/images/project_illustration.png → assets/images/project_illustration.png b/static/images/project_illustration.png → assets/images/project_illustration.png
diff --git a/src/reproduction_2T6S.ipynb → examples/notebooks/reproduction_2T6S.ipynb b/src/reproduction_2T6S.ipynb → examples/notebooks/reproduction_2T6S.ipynb
@@ -42,12 +42,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "id": "digital-intention",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lib import pipelines_2T6S\n",
+    "from narps_open.pipelines import team_2T6S\n",
     "\n",
     "from os.path import join as opj\n",
     "import os\n",
@@ -136,7 +136,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "l1_analysis = pipelines_2T6S.get_l1_analysis(subject_list, TR, fwhm, run_list, exp_dir, \n",
+    "l1_analysis = team_2T6S.get_l1_analysis(subject_list, TR, fwhm, run_list, exp_dir, \n",
     "                                             result_dir, working_dir, output_dir)"
    ]
   },
@@ -177,7 +177,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "l2_analysis_equal_indiff = pipelines_2T6S.get_l2_analysis(subject_list, n_sub, contrast_list, \"equalIndifference\", \n",
+    "l2_analysis_equal_indiff = team_2T6S.get_l2_analysis(subject_list, n_sub, contrast_list, \"equalIndifference\", \n",
     "                                                          exp_dir, result_dir, working_dir, output_dir)"
    ]
   },
@@ -198,7 +198,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "l2_analysis_equal_range = pipelines_2T6S.get_l2_analysis(subject_list, n_sub, contrast_list, \"equalRange\", \n",
+    "l2_analysis_equal_range = team_2T6S.get_l2_analysis(subject_list, n_sub, contrast_list, \"equalRange\", \n",
     "                                                          exp_dir, result_dir, working_dir, output_dir)"
    ]
   },
@@ -219,7 +219,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "l2_analysis_groupcomp = pipelines_2T6S.get_l2_analysis(subject_list, n_sub, contrast_list, \"groupComp\", \n",
+    "l2_analysis_groupcomp = team_2T6S.get_l2_analysis(subject_list, n_sub, contrast_list, \"groupComp\", \n",
     "                                                          exp_dir, result_dir, working_dir, output_dir)"
    ]
   },
@@ -260,7 +260,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.10.9"
   }
  },
  "nbformat": 4,

diff --git a/src/reproduction_4TQ6.ipynb → examples/notebooks/reproduction_4TQ6.ipynb b/src/reproduction_4TQ6.ipynb → examples/notebooks/reproduction_4TQ6.ipynb
diff --git a/src/reproduction_98BT.ipynb → examples/notebooks/reproduction_98BT.ipynb b/src/reproduction_98BT.ipynb → examples/notebooks/reproduction_98BT.ipynb
diff --git a/src/reproduction_C88N.ipynb → examples/notebooks/reproduction_C88N.ipynb b/src/reproduction_C88N.ipynb → examples/notebooks/reproduction_C88N.ipynb
diff --git a/src/reproduction_J7F9.ipynb → examples/notebooks/reproduction_J7F9.ipynb b/src/reproduction_J7F9.ipynb → examples/notebooks/reproduction_J7F9.ipynb
diff --git a/src/reproduction_Q6O0.ipynb → examples/notebooks/reproduction_Q6O0.ipynb b/src/reproduction_Q6O0.ipynb → examples/notebooks/reproduction_Q6O0.ipynb
diff --git a/src/reproduction_R9K3.ipynb → examples/notebooks/reproduction_R9K3.ipynb b/src/reproduction_R9K3.ipynb → examples/notebooks/reproduction_R9K3.ipynb
diff --git a/src/reproduction_T54A.ipynb → examples/notebooks/reproduction_T54A.ipynb b/src/reproduction_T54A.ipynb → examples/notebooks/reproduction_T54A.ipynb
diff --git a/src/reproduction_V55J.ipynb → examples/notebooks/reproduction_V55J.ipynb b/src/reproduction_V55J.ipynb → examples/notebooks/reproduction_V55J.ipynb
diff --git a/src/reproduction_X19V.ipynb → examples/notebooks/reproduction_X19V.ipynb b/src/reproduction_X19V.ipynb → examples/notebooks/reproduction_X19V.ipynb
diff --git a/narps_open/__init__.py b/narps_open/__init__.py
diff --git a/src/models/model-R9K3_smdl.json → narps_open/models/model-R9K3_smdl.json b/src/models/model-R9K3_smdl.json → narps_open/models/model-R9K3_smdl.json
diff --git a/src/models/model-narps_smdl.json → narps_open/models/model-narps_smdl.json b/src/models/model-narps_smdl.json → narps_open/models/model-narps_smdl.json
diff --git a/narps_open/pipelines/__init__.py b/narps_open/pipelines/__init__.py
diff --git a/src/lib/analysis_pipelines_config.tsv → ...n/pipelines/analysis_pipelines_config.tsv b/src/lib/analysis_pipelines_config.tsv → ...n/pipelines/analysis_pipelines_config.tsv
diff --git a/src/lib/pipelines_template.py → narps_open/pipelines/pipelines_template.py b/src/lib/pipelines_template.py → narps_open/pipelines/pipelines_template.py
diff --git a/src/lib/pipelines_0I4U_debug.py → narps_open/pipelines/team_0I4U_debug.py b/src/lib/pipelines_0I4U_debug.py → narps_open/pipelines/team_0I4U_debug.py
diff --git a/src/lib/pipelines_1KB2_debug.py → narps_open/pipelines/team_1KB2_debug.py b/src/lib/pipelines_1KB2_debug.py → narps_open/pipelines/team_1KB2_debug.py
diff --git a/src/lib/pipelines_2T6S.py → narps_open/pipelines/team_2T6S.py b/src/lib/pipelines_2T6S.py → narps_open/pipelines/team_2T6S.py
diff --git a/src/lib/pipelines_43FJ_debug.py → narps_open/pipelines/team_43FJ_debug.py b/src/lib/pipelines_43FJ_debug.py → narps_open/pipelines/team_43FJ_debug.py
diff --git a/src/lib/pipelines_4TQ6_wip.py → narps_open/pipelines/team_4TQ6_wip.py b/src/lib/pipelines_4TQ6_wip.py → narps_open/pipelines/team_4TQ6_wip.py
diff --git a/src/lib/pipelines_98BT.py → narps_open/pipelines/team_98BT.py b/src/lib/pipelines_98BT.py → narps_open/pipelines/team_98BT.py
diff --git a/src/lib/pipelines_C88N.py → narps_open/pipelines/team_C88N.py b/src/lib/pipelines_C88N.py → narps_open/pipelines/team_C88N.py
diff --git a/src/lib/pipelines_J7F9.py → narps_open/pipelines/team_J7F9.py b/src/lib/pipelines_J7F9.py → narps_open/pipelines/team_J7F9.py
diff --git a/src/lib/pipelines_Q6O0.py → narps_open/pipelines/team_Q6O0.py b/src/lib/pipelines_Q6O0.py → narps_open/pipelines/team_Q6O0.py
diff --git a/src/lib/pipelines_R9K3_wip.py → narps_open/pipelines/team_R9K3_wip.py b/src/lib/pipelines_R9K3_wip.py → narps_open/pipelines/team_R9K3_wip.py
diff --git a/src/lib/pipelines_T54A.py → narps_open/pipelines/team_T54A.py b/src/lib/pipelines_T54A.py → narps_open/pipelines/team_T54A.py
diff --git a/src/lib/pipelines_V55J.py → narps_open/pipelines/team_V55J.py b/src/lib/pipelines_V55J.py → narps_open/pipelines/team_V55J.py
diff --git a/src/lib/pipelines_X19V.py → narps_open/pipelines/team_X19V.py b/src/lib/pipelines_X19V.py → narps_open/pipelines/team_X19V.py
diff --git a/src/lib/utils.py → narps_open/utils/__init__.py b/src/lib/utils.py → narps_open/utils/__init__.py
diff --git a/setup.py b/setup.py
@@ -0,0 +1,45 @@
+#!/usr/bin/python
+# coding: utf-8
+
+"""
+Allow the project to be installed as a local package, using :
+    python -m pip install .
+    or
+    python -m pip install -e .
+The -e option stands for editable, which allows to change the
+source code of the package without having to reinstall it. Using this option
+will add the current directory (.) to the system path.
+"""
+
+from setuptools import setup, find_packages
+
+requires = [
+]
+
+setup(
+    name = 'narps_open',
+    version = '0.1.0',
+    description = 'The NARPS open pipelines project :\
+    a codebase reproducing the 70 pipelines of the NARPS study (Botvinik-Nezer et al., 2020).',
+    long_description = 'file: README.md',
+    long_description_content_type = 'text/markdown',
+    author = '',
+    author_email = '',
+    url = 'https://github.com/Inria-Empenn/narps_open_pipelines',
+    include_package_data = True,
+    python_requires = '>=3.8,<3.11',
+    install_requires = requires,
+    classifiers = [
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.8'
+    ],
+    project_urls = {
+        'Bug Tracker': 'https://github.com/Inria-Empenn/narps_open_pipelines/issues',
+        'Source': 'https://github.com/Inria-Empenn/narps_open_pipelines',
+    },
+    packages = find_packages(exclude=('tests', 'examples')),
+    data_files = [
+        ('narps_open/pipelines', ['narps_open/pipelines/analysis_pipelines_config.tsv'])
+    ]
+)
diff --git a/tests/utils/__init__.py b/tests/utils/__init__.py
diff --git a/src/test_utils.py → tests/utils/test_utils.py b/src/test_utils.py → tests/utils/test_utils.py