fixed unused variable issue, other code style issues highlighted by recent Codacy review

monocongo · monocongo · commit 3e1a1ff82bb8 · 2018-12-21T13:04:02.000-05:00
monocongo#240 Former-commit-id: 5acce91
diff --git a/.github/ISSUE_TEMPLATE/Bug_report.md b/.github/ISSUE_TEMPLATE/Bug_report.md
@@ -23,8 +23,8 @@ A clear and concise description of what you expected to happen.
 If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
-- OS: [e.g. iOS]
-- Version: [e.g. 22]
+- OS: \[e.g. iOS]
+- Version: \[e.g. 22]
 
 **Additional context**
 Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/Feature_request.md b/.github/ISSUE_TEMPLATE/Feature_request.md
@@ -1,17 +1,17 @@
----
-name: Feature request
-about: Suggest an idea for this project
-
----
-
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
-
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen.
-
-**Describe alternatives you've considered**
-A clear and concise description of any alternative solutions or features you've considered.
-
-**Additional context**
-Add any other context or screenshots about the feature request here.
+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when \[...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
diff --git a/.idea/climate_indices.iml b/.idea/climate_indices.iml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -9,7 +9,7 @@ Hopefully a clear, coherent style will emerge from a reading of the code. We opt
 * Indent using four spaces (no tabs)
 * Whitespaces after list items and method parameters (`[1, 2, 3]`, not `[1,2,3]`), around operators (`x += 1`, not `x+=1`), and around hash arrows.
 * Liberal use of whitespace and blank lines
-* Comment as much as necessary, more is better than less, and comments are code -- maintain the commentary as if it were being compiled
+* Comment as much as necessary, more is better than less, and comments are code \-- maintain the commentary as if it were being compiled
 * Underscores instead of camelCase
 * This is open source software. Consider the people who will read your code, and make it look nice for them. It's sort of like driving a car: Perhaps you love doing donuts when you're alone, but with passengers the goal is to make the ride as smooth as possible.
 
@@ -62,7 +62,7 @@ Then merge the changes that you fetched:
 For more info, see http://help.github.com/fork-a-repo/
 
 ## How to get your pull request accepted
-We want your submission. But we also want to provide a stable experience for our users and the community. 
+We want your submission. But we also want to provide a stable experience for our users and the community.
 Follow these rules and you should succeed without a problem.
 
 ### Run the tests
@@ -83,7 +83,7 @@ Also, keep your tests as simple as possible. Complex tests end up requiring thei
 Always write a clear log message for your commits. One-line messages are fine for small changes, but bigger changes should look like this:
 
 `$ git commit -m "A brief summary of the commit
-    \> 
+    \>
     \> A paragraph describing what changed and its impact.`
 
 ### Don’t mix code changes with whitespace cleanup
diff --git a/README.md b/README.md
@@ -6,54 +6,53 @@
 
 # Climate Indices in Python
 
-This project contains Python implementations of various climate index algorithms which provide 
+This project contains Python implementations of various climate index algorithms which provide
 a geographical and temporal picture of the severity of precipitation and temperature anomalies
 useful for climate monitoring and research.
 
 The following indices are provided:
 
--  [SPI](https://climatedataguide.ucar.edu/climate-data/standardized-precipitation-index-spi),
-   Standardized Precipitation Index, utilizing both gamma and Pearson Type III distributions
--  [SPEI](https://www.researchgate.net/publication/252361460_The_Standardized_Precipitation-Evapotranspiration_Index_SPEI_a_multiscalar_drought_index),
-   Standardized Precipitation Evapotranspiration Index, utilizing both gamma and Pearson Type III distributions
--  [PET](https://www.ncdc.noaa.gov/monitoring-references/dyk/potential-evapotranspiration),
-   Potential Evapotranspiration, utilizing either [Thornthwaite](http://dx.doi.org/10.2307/21073)
-   or [Hargreaves](http://dx.doi.org/10.13031/2013.26773) equations 
--  [PDSI](http://www.droughtmanagement.info/palmer-drought-severity-index-pdsi/),
-   Palmer Drought Severity Index
--  [scPDSI](http://www.droughtmanagement.info/self-calibrated-palmer-drought-severity-index-sc-pdsi/),
-   Self-calibrated Palmer Drought Severity Index
--  [PHDI](http://www.droughtmanagement.info/palmer-hydrological-drought-index-phdi/),
-   Palmer Hydrological Drought Index
--  [Z-Index](http://www.droughtmanagement.info/palmer-z-index/),
-   Palmer moisture anomaly index (Z-index)
--  [PMDI](https://climate.ncsu.edu/climate/climdiv), Palmer Modified
-   Drought Index
--  [PNP](http://www.droughtmanagement.info/percent-of-normal-precipitation/),
-   Percentage of Normal Precipitation
-
-This Python implementation of the above climate index algorithms is being developed 
+  - [SPI](https://climatedataguide.ucar.edu/climate-data/standardized-precipitation-index-spi),
+    Standardized Precipitation Index, utilizing both gamma and Pearson Type III distributions
+  - [SPEI](https://www.researchgate.net/publication/252361460_The_Standardized_Precipitation-Evapotranspiration_Index_SPEI_a_multiscalar_drought_index),
+    Standardized Precipitation Evapotranspiration Index, utilizing both gamma and Pearson Type III distributions
+  - [PET](https://www.ncdc.noaa.gov/monitoring-references/dyk/potential-evapotranspiration), Potential Evapotranspiration, utilizing either [Thornthwaite](http://dx.doi.org/10.2307/21073)
+    or [Hargreaves](http://dx.doi.org/10.13031/2013.26773) equations
+  - [PDSI](http://www.droughtmanagement.info/palmer-drought-severity-index-pdsi/),
+    Palmer Drought Severity Index
+  - [scPDSI](http://www.droughtmanagement.info/self-calibrated-palmer-drought-severity-index-sc-pdsi/),
+    Self-calibrated Palmer Drought Severity Index
+  - [PHDI](http://www.droughtmanagement.info/palmer-hydrological-drought-index-phdi/),
+    Palmer Hydrological Drought Index
+  - [Z-Index](http://www.droughtmanagement.info/palmer-z-index/),
+    Palmer moisture anomaly index (Z-index)
+  - [PMDI](https://climate.ncsu.edu/climate/climdiv), Palmer Modified
+    Drought Index
+  - [PNP](http://www.droughtmanagement.info/percent-of-normal-precipitation/),
+    Percentage of Normal Precipitation
+
+This Python implementation of the above climate index algorithms is being developed
 with the following goals in mind:
 
--  to provide an open source software package to compute a suite of
-   climate indices commonly used for climate monitoring, with well
-   documented code that is faithful to the relevant literature and
-   which produces scientifically verifiable results
--  to provide a central, open location for participation and collaboration 
-   for researchers, developers, and users of climate indices
--  to facilitate standardization and consensus on best-of-breed
-   climate index algorithms and corresponding compliant implementations in Python
--  to provide transparency into the operational code used for climate
-   monitoring activities at NCEI/NOAA, and consequent reproducibility 
-   of published datasets computed from this package
--  to incorporate modern software engineering principles and programming 
-   best practices
-
-
-This is a developmental/forked version of code that is originally developed and 
-maintained by NIDIS/NCEI/NOAA. The official release version is available at 
+  - to provide an open source software package to compute a suite of
+    climate indices commonly used for climate monitoring, with well
+    documented code that is faithful to the relevant literature and
+    which produces scientifically verifiable results
+  - to provide a central, open location for participation and collaboration
+    for researchers, developers, and users of climate indices
+  - to facilitate standardization and consensus on best-of-breed
+    climate index algorithms and corresponding compliant implementations in Python
+  - to provide transparency into the operational code used for climate
+    monitoring activities at NCEI/NOAA, and consequent reproducibility
+    of published datasets computed from this package
+  - to incorporate modern software engineering principles and programming
+    best practices
+
+
+This is a developmental/forked version of code that is originally developed and
+maintained by NIDIS/NCEI/NOAA. The official release version is available at
 [drought.gov](https://www.drought.gov/drought/python-climate-indices).
 
-* [__Documentation__](https://climate-indices.readthedocs.io/en/latest/)
-* [__License__](LICENSE)
-* [__Disclaimer__](DISCLAIMER)
+  - [__Documentation__](https://climate-indices.readthedocs.io/en/latest/)
+  - [__License__](LICENSE)
+  - [__Disclaimer__](DISCLAIMER)
diff --git a/scripts/process_divisions.py b/scripts/process_divisions.py
@@ -535,9 +535,8 @@ def process_divisions(
 
 # ----------------------------------------------------------------------------------------------------------------------
 if __name__ == "__main__":
-    """
-    This module is used to perform climate indices processing on nClimGrid datasets in NetCDF.
-    """
+
+    # This module is used to perform climate indices processing on nClimGrid datasets in NetCDF.
 
     try:
 
diff --git a/scripts/process_grid.py b/scripts/process_grid.py
@@ -1029,23 +1029,23 @@ def _parallel_process(index, arrays_dict, input_var_names, output_var_name, args
     ) as pool:
 
         """
-         the function _unpacking_apply_along_axis() being applied in Pool.map() is separate
+         the function _apply_along_axis() being applied in Pool.map() is separate
          so that subprocesses can import it, and is simply a thin wrapper that handles the
          fact that Pool.map() only takes a single argument:
         """
 
         if index in ["spei", "pet"]:
-            pool.map(_unpacking_apply_along_axis_double, chunk_params)
+            pool.map(_apply_along_axis_double, chunk_params)
         elif index == "palmers":
-            pool.map(_unpacking_apply_along_axis_palmers, chunk_params)
+            pool.map(_apply_along_axis_palmers, chunk_params)
         else:
-            pool.map(_unpacking_apply_along_axis, chunk_params)
+            pool.map(_apply_along_axis, chunk_params)
 
 
 # ------------------------------------------------------------------------------
-def _unpacking_apply_along_axis(params):
+def _apply_along_axis(params):
     """
-    Like numpy.apply_along_axis(), but and with arguments in a dict instead.
+    Like numpy.apply_along_axis(), but with arguments in a dict instead.
     Applicable for applying a function across subarrays of a single input array.
 
     This function is useful with multiprocessing.Pool().map(): (1) map() only
@@ -1075,9 +1075,9 @@ def _unpacking_apply_along_axis(params):
 
 
 # ------------------------------------------------------------------------------
-def _unpacking_apply_along_axis_double(params):
+def _apply_along_axis_double(params):
     """
-    Like numpy.apply_along_axis(), but and with arguments in a dict instead.
+    Like numpy.apply_along_axis(), but with arguments in a dict instead.
     Applicable for applying a function across subarrays of two input arrays.
 
     This function is useful with multiprocessing.Pool().map(): (1) map() only
@@ -1130,9 +1130,9 @@ def _unpacking_apply_along_axis_double(params):
 
 
 # ------------------------------------------------------------------------------
-def _unpacking_apply_along_axis_palmers(params):
+def _apply_along_axis_palmers(params):
     """
-    Like numpy.apply_along_axis(), but and with arguments in a dict instead.
+    Like numpy.apply_along_axis(), but with arguments in a dict instead.
     Applicable for applying a function across subarrays of Palmer-specific
     input arrays.
 
@@ -1249,21 +1249,20 @@ def _prepare_file(netcdf_file, var_name):
 
 # ------------------------------------------------------------------------------
 if __name__ == "__main__":
-    """
-    This script is used to perform climate indices processing on NetCDF 
-    gridded datasets.
-
-    Example command line arguments for SPI only using monthly precipitation input:
-
-    --index spi
-    --periodicity monthly
-    --scales 1 2 3 6 9 12 24
-    --calibration_start_year 1998
-    --calibration_end_year 2016
-    --netcdf_precip example_data/nclimgrid_prcp_lowres.nc
-    --var_name_precip prcp
-    --output_file_base ~/data/test/spi/nclimgrid_lowres
-    """
+
+    # This script is used to perform climate indices processing on NetCDF
+    # gridded datasets.
+    #
+    # Example command line arguments for SPI only using monthly precipitation input:
+    #
+    # --index spi
+    # --periodicity monthly
+    # --scales 1 2 3 6 9 12 24
+    # --calibration_start_year 1998
+    # --calibration_end_year 2016
+    # --netcdf_precip example_data/nclimgrid_prcp_lowres.nc
+    # --var_name_precip prcp
+    # --output_file_base ~/data/test/spi/nclimgrid_lowres
 
     try:
 
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -284,6 +284,16 @@ def palmer_pdsi_monthly():
     )
 
 
+@pytest.fixture(scope="module")
+def palmer_pdsi_from_scpdsi_monthly():
+
+    return np.load(
+        os.path.join(
+            os.path.split(__file__)[0], "fixture", "palmer_pdsi_from_scpdsi.npy"
+        )
+    )
+
+
 @pytest.fixture(scope="module")
 def palmer_phdi_monthly():
 
diff --git a/tests/fixture/palmer_pdsi_from_scpdsi.npy b/tests/fixture/palmer_pdsi_from_scpdsi.npy
diff --git a/tests/test_compute.py b/tests/test_compute.py
@@ -5,12 +5,12 @@
 
 from climate_indices import compute
 
-# ----------------------------------------------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 # disable logging messages
 logging.disable(logging.CRITICAL)
 
 
-# ----------------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
 @pytest.mark.usefixtures(
     "precips_mm_monthly",
     "precips_mm_daily",
diff --git a/tests/test_eto.py b/tests/test_eto.py
@@ -11,11 +11,6 @@
 logging.disable(logging.CRITICAL)
 
 
-"""
-Tests for `eto.py`.
-"""
-
-
 # ------------------------------------------------------------------------------------------------------------------
 def test_eto_hargreaves():
 
diff --git a/tests/test_indices.py b/tests/test_indices.py
@@ -10,9 +10,7 @@
 logging.disable(logging.CRITICAL)
 
 
-"""
-Tests for `indices.py`.
-"""
+# Tests for `climate_indices.indices.py`.
 
 
 # ---------------------------------------------------------------------------------------
diff --git a/tests/test_netcdf_utils.py b/tests/test_netcdf_utils.py
@@ -10,9 +10,7 @@
 logging.disable(logging.CRITICAL)
 
 
-"""
-Tests for `netcdf_utils.py`.
-"""
+# Tests for `scripts.netcdf_utils.py`
 
 
 # ---------------------------------------------------------------------------------------
diff --git a/tests/test_palmer.py b/tests/test_palmer.py
@@ -10,9 +10,7 @@
 logging.disable(logging.CRITICAL)
 
 
-"""
-Tests for `palmer.py`.
-"""
+# Tests for `climate_indices.palmer.py`
 
 
 # ---------------------------------------------------------------------------------------
@@ -287,6 +285,7 @@ def test_cafec_compute_X(palmer_zindex_monthly):
     "data_year_start_monthly",
     "calibration_year_start_monthly",
     "calibration_year_end_monthly",
+    "palmer_pdsi_from_scpdsi_monthly",
     "palmer_scpdsi_monthly",
     "palmer_scphdi_monthly",
     "palmer_scpmdi_monthly",
@@ -299,6 +298,7 @@ def test_scpdsi(
     data_year_start_monthly,
     calibration_year_start_monthly,
     calibration_year_end_monthly,
+    palmer_pdsi_from_scpdsi_monthly,
     palmer_scpdsi_monthly,
     palmer_scphdi_monthly,
     palmer_scpmdi_monthly,
@@ -325,6 +325,14 @@ def test_scpdsi(
         err_msg="PDSI not computed as expected from monthly inputs",
     )
 
+    np.testing.assert_allclose(
+        pdsi,
+        palmer_pdsi_from_scpdsi_monthly,
+        atol=0.001,
+        equal_nan=True,
+        err_msg="PDSI not computed as expected from monthly inputs",
+    )
+
     np.testing.assert_allclose(
         phdi,
         palmer_scphdi_monthly,
