Merge pull request #6 from isi-nmr/dev

Version 0.1.3

.github/workflows/python-ci.yml

@@ -15,43 +15,49 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install pytest
         pip install zenodo_get
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
     - name: Install brukerapi
       run: |
         git clone -b dev https://github.com/isi-nmr/brukerapi-python.git
         cd brukerapi-python
         python setup.py build
         python setup.py install
 
-    - name: Test using the bruker2nifti_qa data set
-      run: |
-        cd brukerapi-python/test
-        git clone https://gitlab.com/naveau/bruker2nifti_qa.git
-        python -m pytest --test_data bruker2nifti_qa/raw --test_config config/auto_test_qa.json -v
-
-    - name: Test using the PV5.1 test data set
-      run: |
-        cd brukerapi-python/test
-        zenodo_get 10.5281/zenodo.3899268
-        unzip 0.2H2.zip
-        python -m pytest . --test_data "0.2H2" --test_config "config/auto_test_pv51.json" -v
-
-    - name: Test using the PV6.0.1 test data set
-      run: |
-        cd brukerapi-python/test
-        zenodo_get 10.5281/zenodo.3894651
-        unzip 20200612_094625_lego_phantom_3_1_2.zip
-        python -m pytest --test_data "20200612_094625_lego_phantom_3_1_2" --test_config "config/auto_test_pv601.json" -v
+#TODO at this point the CI only checks the ability to install the API, the tests will be revisited in the next version
+#    - name: Download test data from Zenodo
+#      run: |
+#        cd brukerapi-python/test
+#        zenodo_get 10.5281/zenodo.4522220
+#
+#    - name: Test using the PV5.1 data set
+#      run: |
+#        cd brukerapi-python/test
+#        unzip 0.2H2.zip
+#        python -m pytest . --test_data "0.2H2" --test_suites="test_parameters test_properties test_data" -v
+#
+#    - name: Test using the PV6.0.1 data set
+#      run: |
+#        cd brukerapi-python/test
+#        unzip 20200612_094625_lego_phantom_3_1_2.zip
+#        python -m pytest --test_data "20200612_094625_lego_phantom_3_1_2"  --test_suites="test_parameters test_properties test_data" -v
+
+#    - name: Test using the PV7.0.0 data set
+#      run: |
+#        cd brukerapi-python/test
+#        unzip 20210128_122257_LEGO_PHANTOM_API_TEST_1_1.zip
+#        python -m pytest --test_data "20210128_122257_LEGO_PHANTOM_API_TEST_1_1" --test_suites="test_parameters test_data" -v

.gitignore

@@ -139,4 +139,5 @@ brukerapi/tests/results/
 test/results
 
 # tmp
-examples/tmp/
+examples/tmp/
+examples/demo.py

.run/test_pv_51.run.xml

@@ -0,0 +1,22 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="test_pv_51" type="tests" factoryName="py.test">
+    <module name="brukerapi-python" />
+    <option name="INTERPRETER_OPTIONS" value="" />
+    <option name="PARENT_ENVS" value="true" />
+    <envs>
+      <env name="PATH_DATA" value="$USER_HOME$/data_clean" />
+    </envs>
+    <option name="SDK_HOME" value="/usr/bin/python3.8" />
+    <option name="WORKING_DIRECTORY" value="" />
+    <option name="IS_MODULE_SDK" value="false" />
+    <option name="ADD_CONTENT_ROOTS" value="true" />
+    <option name="ADD_SOURCE_ROOTS" value="true" />
+    <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
+    <option name="_new_keywords" value="&quot;&quot;" />
+    <option name="_new_parameters" value="&quot;&quot;" />
+    <option name="_new_additionalArguments" value="&quot;--test_data\u003d${PATH_DATA}/0.2H2 --test_suites\u003d\&quot;test_parameters test_properties test_data\&quot;&quot;" />
+    <option name="_new_target" value="&quot;test.test_dataset&quot;" />
+    <option name="_new_targetType" value="&quot;PYTHON&quot;" />
+    <method v="2" />
+  </configuration>
+</component>

.run/test_pv_601.run.xml

@@ -0,0 +1,22 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="test_pv_601" type="tests" factoryName="py.test">
+    <module name="brukerapi-python" />
+    <option name="INTERPRETER_OPTIONS" value="" />
+    <option name="PARENT_ENVS" value="true" />
+    <envs>
+      <env name="PATH_DATA" value="$USER_HOME$/data_clean" />
+    </envs>
+    <option name="SDK_HOME" value="/usr/bin/python3.8" />
+    <option name="WORKING_DIRECTORY" value="" />
+    <option name="IS_MODULE_SDK" value="false" />
+    <option name="ADD_CONTENT_ROOTS" value="true" />
+    <option name="ADD_SOURCE_ROOTS" value="true" />
+    <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
+    <option name="_new_keywords" value="&quot;&quot;" />
+    <option name="_new_parameters" value="&quot;&quot;" />
+    <option name="_new_additionalArguments" value="&quot;--test_data\u003d${PATH_DATA}/20200612_094625_lego_phantom_3_1_2 --test_suites\u003d\&quot;test_parameters test_properties test_data\&quot;&quot;" />
+    <option name="_new_target" value="&quot;test.test_dataset&quot;" />
+    <option name="_new_targetType" value="&quot;PYTHON&quot;" />
+    <method v="2" />
+  </configuration>
+</component>

.run/test_pv_700.run.xml

@@ -0,0 +1,22 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="test_pv_700" type="tests" factoryName="py.test">
+    <module name="brukerapi-python" />
+    <option name="INTERPRETER_OPTIONS" value="" />
+    <option name="PARENT_ENVS" value="true" />
+    <envs>
+      <env name="PATH_DATA" value="$USER_HOME$/data_clean" />
+    </envs>
+    <option name="SDK_HOME" value="/usr/bin/python3.8" />
+    <option name="WORKING_DIRECTORY" value="" />
+    <option name="IS_MODULE_SDK" value="false" />
+    <option name="ADD_CONTENT_ROOTS" value="true" />
+    <option name="ADD_SOURCE_ROOTS" value="true" />
+    <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
+    <option name="_new_keywords" value="&quot;&quot;" />
+    <option name="_new_parameters" value="&quot;&quot;" />
+    <option name="_new_additionalArguments" value="&quot;--test_data\u003d${PATH_DATA}/20210128_122257_LEGO_PHANTOM_API_TEST_1_1 --test_suites\u003d\&quot;test_parameters test_data\&quot;&quot;" />
+    <option name="_new_target" value="&quot;test.test_dataset&quot;" />
+    <option name="_new_targetType" value="&quot;PYTHON&quot;" />
+    <method v="2" />
+  </configuration>
+</component>

CHANGELOG.rst

@@ -3,6 +3,12 @@ Change Log
 
 Log of changes of the Python Bruker API project.
 
+0.1.3 (2020-02-11)
+-------------------
+- Support for ParaVision 7.0
+- TE and TR properties for fid dataset type
+- Beta version of the affine property for 2dseq files
+
 0.1.2 (2020-11-17)
 -------------------
 - Revision of CLI

MANIFEST.in

@@ -1,8 +1,8 @@
-include brukerapi/config/schema_2dseq_core.json
-include brukerapi/config/schema_2dseq_custom.json
-include brukerapi/config/schema_fid_core.json
-include brukerapi/config/schema_fid_custom.json
-include brukerapi/config/schema_rawdata_core.json
-include brukerapi/config/schema_rawdata_custom.json
-include brukerapi/config/schema_traj_core.json
-include brukerapi/config/schema_traj_custom.json
+include brukerapi/config/properties_2dseq_core.json
+include brukerapi/config/properties_2dseq_custom.json
+include brukerapi/config/properties_fid_core.json
+include brukerapi/config/properties_fid_custom.json
+include brukerapi/config/properties_rawdata_core.json
+include brukerapi/config/properties_rawdata_custom.json
+include brukerapi/config/properties_traj_core.json
+include brukerapi/config/properties_traj_custom.json