ewokstomo 0.1.0__tar.gz

ewokstomo-0.1.0/LICENSE.md

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+# MIT License
+
+**Copyright (c) 2024 European Synchrotron Radiation Facility**
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

ewokstomo-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ewokstomo
+Version: 0.1.0
+Summary: Data processing workflows for Tomography
+Author-email: ESRF <dau-pydev@esrf.fr>
+License: # MIT License
+        
+        **Copyright (c) 2024 European Synchrotron Radiation Facility**
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy of
+        this software and associated documentation files (the "Software"), to deal in
+        the Software without restriction, including without limitation the rights to
+        use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+        the Software, and to permit persons to whom the Software is furnished to do so,
+        subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+        FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+        COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+        IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+        CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+        
+Project-URL: Homepage, https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/
+Project-URL: Documentation, https://ewokstomo.readthedocs.io/
+Project-URL: Repository, https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/
+Project-URL: Issues, https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/issues
+Project-URL: Changelog, https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/-/blob/main/CHANGELOG.md
+Keywords: ewoks
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: ewokscore
+Requires-Dist: nxtomomill
+Provides-Extra: test
+Requires-Dist: pytest>=7; extra == "test"
+Requires-Dist: ewoks; extra == "test"
+Provides-Extra: dev
+Requires-Dist: ewokstomo[test]; extra == "dev"
+Requires-Dist: black>=25; extra == "dev"
+Requires-Dist: flake8>=4; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: ewokstomo[test]; extra == "doc"
+Requires-Dist: sphinx>=4.5; extra == "doc"
+Requires-Dist: sphinx-autodoc-typehints>=1.16; extra == "doc"
+Requires-Dist: pydata-sphinx-theme; extra == "doc"
+Dynamic: license-file
+
+# ewokstomo
+
+Data processing workflows for Tomography
+
+## Documentation
+
+https://ewokstomo.readthedocs.io/

ewokstomo-0.1.0/README.md

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+# ewokstomo
+
+Data processing workflows for Tomography
+
+## Documentation
+
+https://ewokstomo.readthedocs.io/

ewokstomo-0.1.0/pyproject.toml

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+[build-system]
+requires = [
+    "setuptools>=61",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "ewokstomo"
+version = "0.1.0"
+keywords = [
+    'ewoks'
+]
+
+authors = [{name = "ESRF", email = "dau-pydev@esrf.fr"}]
+description = "Data processing workflows for Tomography"
+readme = {file = "README.md", content-type = "text/markdown"}
+license = {file = "LICENSE.md"}
+classifiers = [
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: MIT License',
+    'Programming Language :: Python :: 3',
+]
+requires-python = ">=3.8"
+dependencies = [
+    'ewokscore',
+    'nxtomomill',
+]
+
+[project.urls]
+Homepage = "https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/"
+Documentation = "https://ewokstomo.readthedocs.io/"
+Repository = "https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/"
+Issues = "https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/issues"
+Changelog = "https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/-/blob/main/CHANGELOG.md"
+
+[project.optional-dependencies]
+test = [
+    'pytest >=7',
+    'ewoks',
+]
+dev = [
+    "ewokstomo[test]",
+    'black >=25',
+    'flake8 >=4',
+]
+doc = [
+    "ewokstomo[test]",
+    'sphinx >=4.5',
+    'sphinx-autodoc-typehints >=1.16',
+    'pydata-sphinx-theme',
+]
+
+[tool.setuptools]
+package-dir = {''= 'src'}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+namespaces = false
+
+[tool.setuptools.package-data]
+"ewokstomo.tests" = ['data/**/*', 'workflows/*.json']
+
+[project.entry-points."ewoks.tasks.class"]
+"ewokstomo.tasks.*" = "ewokstomo"
+
+
+[tool.coverage.run]
+omit = [
+    "*/tests/*"
+]

ewokstomo-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

ewokstomo-0.1.0/src/ewokstomo/tasks/nxtomomill.py

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+from ewokscore import Task
+import subprocess
+from pathlib import Path
+
+
+class H5ToNx(
+    Task, input_names=["bliss_hdf5_path", "output_dir"], output_names=["result"]
+):
+
+    def run(self):
+        """
+        Executes a subprocess that runs nxtomomill to convert the input_scan to nx format
+        :return: The path to the created nx file
+        """
+
+        command = [
+            "nxtomomill",
+            "h52nx",
+            self.inputs.bliss_hdf5_path,
+            self.inputs.output_dir,
+        ]
+        subprocess.run(command, capture_output=True, text=True, check=True)
+        input_path = Path(self.inputs.bliss_hdf5_path)
+        output_dir = Path(self.inputs.output_dir)
+        new_filename = input_path.stem + ".nx"
+        self.outputs.result = str(output_dir / new_filename)

ewokstomo-0.1.0/src/ewokstomo/tasks/sumtask.py

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+import time
+from ewokscore import Task
+
+
+class SumTask(
+    Task,
+    input_names=["a"],
+    optional_input_names=["b", "delay"],
+    output_names=["result"],
+):
+    """Add two numbers"""
+
+    def run(self):
+        result = self.inputs.a + self.get_input_value("b", 0)
+        time.sleep(self.get_input_value("delay", 0))
+        self.outputs.result = result
+
+
+class SumTask1(
+    Task,
+    input_names=["a"],
+    optional_input_names=["b", "delay"],
+    output_names=["result"],
+):
+    """Add two numbers"""
+
+    def run(self):
+        result = self.inputs.a + self.get_input_value("b", 0)
+        time.sleep(self.get_input_value("delay", 0))
+        self.outputs.result = result
+
+
+class SumTask2(
+    Task,
+    input_names=["a"],
+    optional_input_names=["b", "delay"],
+    output_names=["result"],
+):
+    """Add two numbers"""
+
+    def run(self):
+        result = self.inputs.a + self.get_input_value("b", 0)
+        time.sleep(self.get_input_value("delay", 0))
+        self.outputs.result = result

ewokstomo-0.1.0/src/ewokstomo/tests/test_nxtomo.py

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+import pytest
+import sys
+from ewokstomo.tasks.nxtomomill import H5ToNx
+from ewoks import execute_graph
+from pathlib import Path
+import importlib.resources as pkg_resources
+
+
+def get_json_file(file_name):
+    if sys.version_info >= (3, 10):
+        file_path = pkg_resources.files("ewokstomo.tests.workflows").joinpath(file_name)
+    else:
+        file_path = Path(__file__).parent / "workflows" / file_name
+    return file_path
+
+
+def get_data_file(file_name):
+    if sys.version_info >= (3, 10):
+        file_path = pkg_resources.files(f"ewokstomo.tests.data.{file_name}").joinpath(
+            f"{file_name}.h5"
+        )
+    else:
+        file_path = Path(__file__).parent / "data" / file_name / f"{file_name}.h5"
+    return file_path
+
+
+@pytest.mark.parametrize("Task", [H5ToNx])
+def test_nxtomomill(Task, tmpdir):
+    output_dir = tmpdir / "output"
+    output_dir.mkdir()
+    h5_file_path = get_data_file("TestEwoksTomo_0010")
+
+    task = Task(
+        inputs={
+            "bliss_hdf5_path": h5_file_path,
+            "output_dir": str(output_dir),
+        }
+    )
+    task.run()
+    expected_output = output_dir / "TestEwoksTomo_0010.nx"
+    assert str(Path(task.outputs.result).resolve()) == str(expected_output)
+    # assert Path(expected_output).is_file()
+
+
+@pytest.mark.parametrize("workflow", ["nxtomomill.json"])
+def test_nxtomomill_workflow(workflow, tmpdir):
+    output_dir = tmpdir / "output"
+    output_dir.mkdir()
+    h5_file_path = get_data_file("TestEwoksTomo_0010")
+    workflow_file_path = get_json_file(workflow)
+
+    output = execute_graph(
+        workflow_file_path,
+        inputs=[
+            {
+                "name": "bliss_hdf5_path",
+                "value": h5_file_path,
+            },
+            {"name": "output_dir", "value": str(output_dir)},
+        ],
+    )
+    expected_output = output_dir / "TestEwoksTomo_0010.nx"
+    assert str(Path(output["result"]).resolve()) == str(expected_output)
+    # assert Path(expected_output).is_file()

ewokstomo-0.1.0/src/ewokstomo/tests/test_sumtask.py

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+import pytest
+from ewokstomo.tasks.sumtask import SumTask, SumTask1, SumTask2
+
+
+@pytest.mark.parametrize("Task", [SumTask, SumTask1, SumTask2])
+def test_sum_task(Task):
+    task = Task(inputs={"a": 1, "b": 2})
+    task.run()
+    assert task.outputs.result == 3

ewokstomo-0.1.0/src/ewokstomo/tests/workflows/nxtomomill.json

@@ -0,0 +1,18 @@
+{
+  "directed": true,
+  "multigraph": false,
+  "graph": {
+    "id": "nxtomomill",
+    "schema_version": "1.1",
+    "requirements": [
+    ]
+  },
+  "nodes": [
+    {
+      "task_type": "class",
+      "task_identifier": "tasks.nxtomomill.H5ToNx",
+      "id": "nxtomomill_task"
+    }
+  ],
+  "links": []
+}

ewokstomo-0.1.0/src/ewokstomo.egg-info/PKG-INFO

@@ -0,0 +1,61 @@
+Metadata-Version: 2.4
+Name: ewokstomo
+Version: 0.1.0
+Summary: Data processing workflows for Tomography
+Author-email: ESRF <dau-pydev@esrf.fr>
+License: # MIT License
+        
+        **Copyright (c) 2024 European Synchrotron Radiation Facility**
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy of
+        this software and associated documentation files (the "Software"), to deal in
+        the Software without restriction, including without limitation the rights to
+        use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+        the Software, and to permit persons to whom the Software is furnished to do so,
+        subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+        FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+        COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+        IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+        CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+        
+Project-URL: Homepage, https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/
+Project-URL: Documentation, https://ewokstomo.readthedocs.io/
+Project-URL: Repository, https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/
+Project-URL: Issues, https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/issues
+Project-URL: Changelog, https://gitlab.esrf.fr/workflow/ewoksapps/ewokstomo/-/blob/main/CHANGELOG.md
+Keywords: ewoks
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: ewokscore
+Requires-Dist: nxtomomill
+Provides-Extra: test
+Requires-Dist: pytest>=7; extra == "test"
+Requires-Dist: ewoks; extra == "test"
+Provides-Extra: dev
+Requires-Dist: ewokstomo[test]; extra == "dev"
+Requires-Dist: black>=25; extra == "dev"
+Requires-Dist: flake8>=4; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: ewokstomo[test]; extra == "doc"
+Requires-Dist: sphinx>=4.5; extra == "doc"
+Requires-Dist: sphinx-autodoc-typehints>=1.16; extra == "doc"
+Requires-Dist: pydata-sphinx-theme; extra == "doc"
+Dynamic: license-file
+
+# ewokstomo
+
+Data processing workflows for Tomography
+
+## Documentation
+
+https://ewokstomo.readthedocs.io/

ewokstomo-0.1.0/src/ewokstomo.egg-info/SOURCES.txt

@@ -0,0 +1,36 @@
+LICENSE.md
+README.md
+pyproject.toml
+src/ewokstomo/__init__.py
+src/ewokstomo.egg-info/PKG-INFO
+src/ewokstomo.egg-info/SOURCES.txt
+src/ewokstomo.egg-info/dependency_links.txt
+src/ewokstomo.egg-info/entry_points.txt
+src/ewokstomo.egg-info/requires.txt
+src/ewokstomo.egg-info/top_level.txt
+src/ewokstomo/tasks/__init__.py
+src/ewokstomo/tasks/nxtomomill.py
+src/ewokstomo/tasks/sumtask.py
+src/ewokstomo/tests/__init__.py
+src/ewokstomo/tests/test_nxtomo.py
+src/ewokstomo/tests/test_sumtask.py
+src/ewokstomo/tests/data/TestEwoksTomo_0010/TestEwoksTomo_0010.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0002/edgetwinmic_0000.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0003/edgetwinmic_0000.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0000.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0001.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0002.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0003.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0004.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0005.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0006.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0007.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0008.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0009.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0004/edgetwinmic_0010.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0005/edgetwinmic_0000.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0005/edgetwinmic_0001.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0005/edgetwinmic_0002.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0005/edgetwinmic_0003.h5
+src/ewokstomo/tests/data/TestEwoksTomo_0010/scan0005/edgetwinmic_0004.h5
+src/ewokstomo/tests/workflows/nxtomomill.json

ewokstomo-0.1.0/src/ewokstomo.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

ewokstomo-0.1.0/src/ewokstomo.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[ewoks.tasks.class]
+ewokstomo.tasks.* = ewokstomo

ewokstomo-0.1.0/src/ewokstomo.egg-info/requires.txt

@@ -0,0 +1,17 @@
+ewokscore
+nxtomomill
+
+[dev]
+ewokstomo[test]
+black>=25
+flake8>=4
+
+[doc]
+ewokstomo[test]
+sphinx>=4.5
+sphinx-autodoc-typehints>=1.16
+pydata-sphinx-theme
+
+[test]
+pytest>=7
+ewoks

ewokstomo-0.1.0/src/ewokstomo.egg-info/top_level.txt

@@ -0,0 +1 @@
+ewokstomo