Get docsring examples running

vergauwenthomas · Sep 2, 2024 · 6de8751 · 6de8751
1 parent be1e7aa
commit 6de8751
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Showing 29 changed files with 1,029 additions and 583 deletions.
diff --git a/deploiment/run_doctests.sh b/deploiment/run_doctests.sh
@@ -10,7 +10,12 @@ cd ${DEPLOY_DIR}
 cd .. #Navigate to workdir
 WORKDIR=$(pwd)
 LOGDIR=${DEPLOY_DIR}/logs
+BIGLOGFILE=${LOGDIR}/all_log
 
+#clear big log file
+rm -f ${BIGLOGFILE}
+
+#clear all specific log files
 rm ${LOGDIR}/DOCtest_output_*_log
 
 
@@ -24,7 +29,7 @@ for t in $modules; do
         module_file=${WORKDIR}/metobs_toolkit/${t}
         echo "Running doctests in ${module_file}"
 
-	python3 -m doctest -o ELLIPSIS -o NORMALIZE_WHITESPACE ${module_file} | tee ${LOGDIR}/DOCtest_output_${t:2:-3}_log
+	python3 ${module_file} 2>&1 | tee -a ${LOGDIR}/DOCtest_output_${t:2:-3}_log ${BIGLOGFILE}
 done
 
 rm ${WORKDIR}/*.pkl #created by doctest

diff --git a/docs/build_doc b/docs/build_doc
@@ -5,14 +5,13 @@
 rm -r _build/*
 rm -r _autosummary/*
 
+
 #sphinx-autogen index.rst
 
 
 
 cd ..
 
-
-
 sphinx-build -a -E -v docs/ docs/_build/
 
 cd docs
diff --git a/metobs_toolkit/analysis.py b/metobs_toolkit/analysis.py
diff --git a/metobs_toolkit/data_import.py b/metobs_toolkit/data_import.py
@@ -251,3 +251,12 @@ class MetobsDataImportError(Exception):
     """Exception raised for errors on importing Data."""
 
     pass
+
+
+# =============================================================================
+# Docstring test
+# =============================================================================
+if __name__ == "__main__":
+    from metobs_toolkit.doctest_fmt import setup_and_run_doctest
+
+    setup_and_run_doctest()
diff --git a/metobs_toolkit/dataset_core.py b/metobs_toolkit/dataset_core.py
@@ -591,7 +591,7 @@ def import_dataset(self, folder_path=None, filename="saved_dataset.pkl"):
         >>> import os
         >>> # Import the dataset
         >>> dataset=empty_dataset.import_dataset(folder_path=os.getcwd(),
-        ...                                      filename='your_saved_dataset.pkl')
+        ...                                      filename='your_saved_dataset.pkl')  # doctest: +SKIP
 
         """
         # check if folder_path is known and exists
@@ -886,6 +886,7 @@ def get_station(self, stationname):
              *0 gaps
              *records range: 2022-09-01 00:00:00+00:00 --> 2022-09-15 23:55:00+00:00 (total duration:  14 days 23:55:00)
              *time zone of the records: UTC
+             *Known GEE datasets for:  ['lcz', 'altitude', 'worldcover', 'ERA5-land']
              *Coordinates are available for all stations.
 
         """
@@ -1186,30 +1187,13 @@ def coarsen_time_resolution(
         vlinder03   0 days 00:05:00
         vlinder04   0 days 00:05:00
         vlinder05   0 days 00:05:00
-        vlinder06   0 days 00:05:00
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+                          ...
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-        Name: dataset_resolution, dtype: timedelta64[ns]
+        Name: dataset_resolution, Length: 28, dtype: timedelta64[ns]
 
         We can coarsen the time resolution to 15 minutes with a maximum
         allowd timestamp shift of 4 minutes.
@@ -1223,30 +1207,13 @@ def coarsen_time_resolution(
         vlinder03   0 days 00:15:00
         vlinder04   0 days 00:15:00
         vlinder05   0 days 00:15:00
-        vlinder06   0 days 00:15:00
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+                          ...
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-        Name: dataset_resolution, dtype: timedelta64[ns]
+        Name: dataset_resolution, Length: 28, dtype: timedelta64[ns]
 
         """
 
@@ -1709,3 +1676,12 @@ class MetobsDatasetError(Exception):
     """Exception raised for errors in the template."""
 
     pass
+
+
+# =============================================================================
+# Docstring test
+# =============================================================================
+if __name__ == "__main__":
+    from metobs_toolkit.doctest_fmt import setup_and_run_doctest
+
+    setup_and_run_doctest()