Add hints for NetCDFcxx not found error; fix typos (#29)

.github/workflows/cicd.yaml

@@ -0,0 +1,56 @@
+##    Checks the code logic, style and more
+# -*- coding: utf-8 -*-
+# Copyright (C) 2023 Benjamin Thomas Schwertfeger
+# Github: https://github.com/btschwertfeger
+#
+# Workflow to apply pre-commit, build, test and upload the docker
+# image(s).
+
+name: CI/CD
+
+on:
+  push:
+    branches:
+      - "**"
+
+concurrency:
+  group: CICD-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  ##  Run the pre-commit content
+  Pre-Commit:
+    uses: ./.github/workflows/_pre_commit.yaml
+
+  ##  Build the BiasAdjustCXX command-line tool
+  ##
+  Build:
+    needs: [Pre-Commit]
+    uses: ./.github/workflows/_build.yaml
+
+  ##    Build the documentation
+  ##
+  Build-Doc:
+    needs: [Pre-Commit]
+    uses: ./.github/workflows/_build_doc.yaml
+    with:
+      os: "ubuntu-latest"
+      python-version: "3.11"
+
+  ## Build the test suite and run the unit tests
+  ##
+  Test:
+    needs: [Pre-Commit]
+    uses: ./.github/workflows/_test.yaml
+
+  ##  Create and upload a docker image
+  ##
+  Docker:
+    if: success() && github.ref == 'refs/heads/dev'
+    needs: [Build, Test]
+    uses: ./.github/workflows/_build_docker.yaml
+    with:
+      TAG: ${{ github.ref_name }}
+    secrets:
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}

.github/workflows/cicd.yml → .github/workflows/release.yaml

@@ -4,35 +4,34 @@
 # Github: https://github.com/btschwertfeger
 #
 # Workflow to apply pre-commit, build, test and upload the docker
-# image(s).
+# image. This job is only triggered during a release.
 
-name: CI/CD
+name: Release
 
 on:
-  push:
-    branches:
-      - "**"
+  release:
+    types: [created]
 
 concurrency:
-  group: CICD-${{ github.ref }}
+  group: Release-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
   ##  Run the pre-commit content
   Pre-Commit:
-    uses: ./.github/workflows/_pre_commit.yml
+    uses: ./.github/workflows/_pre_commit.yaml
 
   ##  Build the BiasAdjustCXX command-line tool
   ##
   Build:
     needs: [Pre-Commit]
-    uses: ./.github/workflows/_build.yml
+    uses: ./.github/workflows/_build.yaml
 
   ##    Build the documentation
   ##
   Build-Doc:
     needs: [Pre-Commit]
-    uses: ./.github/workflows/_build_doc.yml
+    uses: ./.github/workflows/_build_doc.yaml
     with:
       os: "ubuntu-latest"
       python-version: "3.11"
@@ -41,14 +40,13 @@ jobs:
   ##
   Test:
     needs: [Pre-Commit]
-    uses: ./.github/workflows/_test.yml
+    uses: ./.github/workflows/_test.yaml
 
-  ##  Create and upload a docker image
+  ##  Create and upload the tagged docker image
   ##
-  Docker:
-    if: success() && github.ref == 'refs/heads/dev'
+  Docker-tag:
     needs: [Build, Test]
-    uses: ./.github/workflows/_build_docker.yml
+    uses: ./.github/workflows/_build_docker.yaml
     with:
       TAG: ${{ github.ref_name }}
     secrets:
@@ -59,8 +57,7 @@ jobs:
   ##
   Docker-latest:
     needs: [Build, Test]
-    if: success() && github.ref == 'refs/heads/master'
-    uses: ./.github/workflows/_build_docker.yml
+    uses: ./.github/workflows/_build_docker.yaml
     with:
       TAG: latest
     secrets:

.gitignore

@@ -36,6 +36,7 @@
 .ipynb_checkpoints
 build/
 output/
+.vscode/
 *tmp*
 qdm_result.nc
 del/

CHANGELOG.md

@@ -1,5 +1,15 @@
 # Changelog
 
+## [Unreleased](https://github.com/btschwertfeger/BiasAdjustCXX/tree/HEAD)
+
+[Full Changelog](https://github.com/btschwertfeger/BiasAdjustCXX/compare/v1.9.0...HEAD)
+
+**Merged pull requests:**
+
+- Add release workflow [\#27](https://github.com/btschwertfeger/BiasAdjustCXX/pull/27) ([btschwertfeger](https://github.com/btschwertfeger))
+- Clarified difference between stochastic and non-stochastic climate variables in doc and readme [\#26](https://github.com/btschwertfeger/BiasAdjustCXX/pull/26) ([btschwertfeger](https://github.com/btschwertfeger))
+- Added more checks during testing [\#25](https://github.com/btschwertfeger/BiasAdjustCXX/pull/25) ([btschwertfeger](https://github.com/btschwertfeger))
+
 ## [v1.9.0](https://github.com/btschwertfeger/BiasAdjustCXX/tree/v1.9.0) (2023-04-20)
 
 [Full Changelog](https://github.com/btschwertfeger/BiasAdjustCXX/compare/v1.8.1...v1.9.0)

CMakeLists.txt

@@ -31,10 +31,10 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/modules/")
 include(FindNetCDFCxx)
 
 if(netCDFCxx_FOUND)
-    message (STATUS "NetCDFCxx found!")
+    message (STATUS "NetCDFCXX found!")
     include_directories(${NetCDFCxx_INCLUDE_DIRS})
 else()
-    message (FATAL_ERROR "Cannot find NetCDFCxx!")
+    message (FATAL_ERROR "Cannot find NetCDFCXX. Make sure that `ncxx4-config` is globally executable!")
 endif()
 
 add_subdirectory(src)

README.rst

@@ -29,7 +29,7 @@ BiasAdjustCXX command-line tool for the application of fast and efficient bias c
 .. |DOI badge| image:: https://zenodo.org/badge/495881923.svg
    :target: https://zenodo.org/badge/latestdoi/495881923
 
-.. |Publication bage| image:: https://img.shields.io/badge/Publication-doi.org%2F10.1016%2Fj.softx.2023.101379-blue
+.. |Publication badge| image:: https://img.shields.io/badge/Publication-doi.org%2F10.1016%2Fj.softx.2023.101379-blue
    :target: https://doi.org/10.1016/j.softx.2023.101379
 
 .. LINKS
@@ -82,7 +82,7 @@ BiasAdjustCXX command-line tool for the application of fast and efficient bias c
 
 |GitHub badge| |License badge| |C++ badge| |CICD badge|
 |Docker pulls badge| |GCC badge| |CMake badge|
-|Release date badge| |Release tag badge| |DOI badge| |Publication bage|
+|Release date badge| |Release tag badge| |DOI badge| |Publication badge|
 
 **The documentation can be found here: https://biasadjustcxx.readthedocs.io/en/latest.**
 
@@ -186,7 +186,7 @@ Notes regarding the scaling-based techniques
   match the techniques described by `Teutschbein et al. (2012)`_ and `Beyer et al. (2020)`_. On the other hand the
   long-term 31-day interval procedures are customized variations and prevent
   disproportionately high differences in the long-term mean values at the monthly transitions.
-  Thats why the long-term 31-day interval variant is the preferred method and is enabled by
+  That's why the long-term 31-day interval variant is the preferred method and is enabled by
   default for all scaling-based techniques.
 
 
@@ -204,6 +204,7 @@ the BiasAdjustCXX command-line tool.
 
 - NetCDF-4 C++ library (`How to install NetCDF-4 C++`_)
 - CMake v3.10+ (`How to install CMake`_)
+- GNU Make (see https://www.gnu.org/software/make/)
 - [optional] Climate Data Operators (`How to install cdo`_)
 
 Please have a look at the following code blocks that demonstrate how to download, build and install
@@ -228,6 +229,9 @@ The tool can be uninstalled using the following command within the project direc
 After the installation, the tool can be executed using the command listed below. This repository
 also serves example data to test this. See the documentation for more information (https://biasadjustcxx.readthedocs.io/en/latest).
 
+If the netcdf-cxx4 libraries cannot be found - make sure that ``ncxx4-config`` is globally executable, since this tool is used
+to determine the location of these libraries.
+
 .. code:: bash
 
   BiasAdjustCXX \
@@ -244,7 +248,7 @@ also serves example data to test this. See the documentation for more informatio
 Docker 🐳
 ~~~~~~~~~~~~~~~
 
-The execution of BiasAdjustCXX is also possiblie within a Docker container.
+The execution of BiasAdjustCXX is also possible within a Docker container.
 This is the preferred option when the installation of `NetCDF-4 C++`_, `CMake`_ or `BiasAdjustCXX`_
 on the local system is not desired. It also makes easier to access this tool since Docker
 container can run on nearly every operating system.

src/CMethods.cxx

@@ -124,7 +124,7 @@ std::vector<std::vector<float>> CMethods::get_long_term_dayofyear(std::vector<fl
  *
  * @param factor value to check
  * @param max_factor max allowed factor (will be casted to positive value, cannot be zero)
- * @return either `factor` if ths ok or `max_factor`
+ * @return either `factor` if it's ok or `max_factor`
  */
 double CMethods::get_adjusted_scaling_factor(double factor, double max_factor) {
     const double abs_max_factor = std::abs(max_factor);
@@ -339,7 +339,7 @@ void CMethods::Variance_Scaling(
 /**
  * Method to adjust 1-dimensional climate data by the delta method.
  * Based on Beyer, R. and Krapp, M. and Manica, A.: An empirical evaluation of bias
- * correction methods for palaeoclimate simulations (https://doi.org/10.5194/cp-16-1493-2020)
+ * correction methods for paleoclimate simulations (https://doi.org/10.5194/cp-16-1493-2020)
  *
  * NOTE: `v_reference.size()` must be equal to `v_scenario.size()`
  * @param v_output 1D output vector that stores the adjusted time series
@@ -426,8 +426,8 @@ void CMethods::Delta_Method(
 
 /**
  * Returns the probability boundaries based on two input time series
- * -> This is required to compute the bin boundaries for the Probability Density and Cumulative Distribution Funtion.
- * -> Used by Quantile and Quantile Delta Mapping by invoking this funtion to get the bins based on the time
+ * -> This is required to compute the bin boundaries for the Probability Density and Cumulative Distribution Function.
+ * -> Used by Quantile and Quantile Delta Mapping by invoking this function to get the bins based on the time
  *    series of the control period.
  *
  * @param a time series
@@ -534,7 +534,7 @@ void CMethods::Quantile_Mapping(
                 MathUtils::interpolate(v_xbins, contr_cdf, (double)v_scenario[ts], false)
             );  // Eq. 1
 
-        // ? Invert in inversed CDF and return
+        // ? Invert in invers CDF and return
         for (unsigned ts = 0; ts < v_scenario.size(); ts++)
             v_output[ts] = (float)MathUtils::interpolate(ref_cdf, v_xbins, cdf_values[ts], false);  // Eq. 1
 
@@ -544,7 +544,7 @@ void CMethods::Quantile_Mapping(
             cdf_values.push_back((y >= 0) ? y : 0);
         }
 
-        // ? Invert in inversed CDF and return
+        // ? Invert in invers CDF and return
         for (unsigned ts = 0; ts < v_scenario.size(); ts++) {
             float y = (float)MathUtils::interpolate(ref_cdf, v_xbins, cdf_values[ts], true);  // Eq. 1
             v_output[ts] = (y >= 0) ? y : 0;
@@ -621,7 +621,7 @@ void CMethods::Quantile_Delta_Mapping(
     for (unsigned ts = 0; ts < v_scenario.size(); ts++)
         QDM1.push_back(MathUtils::interpolate(ref_cdf, v_xbins, epsilon[ts], false));  // Eq. 1.2
 
-    // ? Invert, insert in inversed CDF and return
+    // ? Invert, insert in invers CDF and return
     if (isAdd) {
         for (unsigned ts = 0; ts < v_scenario.size(); ts++)
             v_output[ts] = (float)(QDM1[ts] + v_scenario[ts] - MathUtils::interpolate(contr_cdf, v_xbins, epsilon[ts], false));  // Eq. 1.3f.

src/MathUtils.cxx

@@ -65,7 +65,7 @@ MathUtils::~MathUtils() {}
 /**
  * Returns the pointer to a function based on `name`
  *
- * @param name name of the desired funtion
+ * @param name name of the desired function
  * @return point to desired funciton
  */
 Func_one MathUtils::get_method_for_1_ds(std::string name) {
@@ -81,8 +81,8 @@ Func_one MathUtils::get_method_for_1_ds(std::string name) {
 /**
  * Returns the pointer to a function based on `name`
  *
- * @param name name of the desired funtion
- * @return point to desired funciton
+ * @param name name of the desired function
+ * @return point to desired function
  */
 Func_two MathUtils::get_method_for_2_ds(std::string name) {
     if (name == "rmse")

src/main.cxx

@@ -54,7 +54,7 @@
  */
 
 /**
- * Command-line output of the duraton between a start time
+ * Command-line output of the duration between a start time
  *
  * @param start_time start time to calculate the duration
  */