Merge pull request #8 from jacobwilliams/develop

Develop

Author: jacobwilliams

.github/workflows/CI.yml

@@ -8,8 +8,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        gcc_v: [9] # Version of GFortran we want to use.
-        python-version: [3.7]
+        gcc_v: [10] # Version of GFortran we want to use.
+        python-version: [3.9]
     env:
       FC: gfortran-${{ matrix.gcc_v }}
       GCC_V: ${{ matrix.gcc_v }}
@@ -29,32 +29,45 @@ jobs:
       uses: ts-graphviz/setup-graphviz@v1
 
     - name: Setup Fortran Package Manager
-      uses: fortran-lang/setup-fpm@v3
+      uses: fortran-lang/setup-fpm@v4
       with:
         github-token: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Install Python dependencies
       if: contains( matrix.os, 'ubuntu')
       run: |
         python -m pip install --upgrade pip
-        pip install ford 
+        pip install matplotlib ford 
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
     - name: Install GFortran Linux
       if: contains( matrix.os, 'ubuntu')
       run: |
-        sudo add-apt-repository ppa:ubuntu-toolchain-r/test
-        sudo apt-get update
-        sudo apt-get install -y gcc-${GCC_V} gfortran-${GCC_V}
-        sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100 \
-        --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V} \
-        --slave /usr/bingcov gcov /usr/bin/gcov-${GCC_V}
+        sudo apt-get install lcov
+        sudo update-alternatives \
+           --install /usr/bin/gcc gcc /usr/bin/gcc-${{ matrix.gcc_v }} 100 \
+           --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${{ matrix.gcc_v }} \
+           --slave /usr/bin/gcov gcov /usr/bin/gcov-${{ matrix.gcc_v }}
 
-    - name: Compile
-      run: fpm build --profile release
+    # - name: Compile
+    #   run: fpm build --profile release
 
     - name: Run tests
-      run: fpm test
+      run: fpm test --profile debug --flag -coverage
+
+    - name: Create coverage report
+      run: |
+        mkdir -p ${{ env.COV_DIR }}
+        lcov --capture --initial --base-directory . --directory build/gfortran_*/ --output-file ${{ env.COV_DIR }}/coverage.base
+        lcov --capture --base-directory . --directory build/gfortran_*/ --output-file ${{ env.COV_DIR }}/coverage.capture
+        lcov --add-tracefile ${{ env.COV_DIR }}/coverage.base --add-tracefile ${{ env.COV_DIR }}/coverage.capture --output-file ${{ env.COV_DIR }}/coverage.info
+      env:
+        COV_DIR: build/coverage
+
+    - name: Upload coverage report
+      uses: codecov/codecov-action@v2
+      with:
+        files: build/coverage/coverage.info
 
     - name: Build documentation
       run: ford ./numdiff.md

LICENSE

@@ -1,7 +1,7 @@
 NumDiff -- Numerical Differentiation Library
 https://github.com/jacobwilliams/NumDiff
 
-Copyright (c) 2016-2021, Jacob Williams
+Copyright (c) 2016-2022, Jacob Williams
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

README.md

@@ -7,7 +7,9 @@
 
 ## Status
 
+[![GitHub release](https://img.shields.io/github/release/jacobwilliams/NumDiff.svg?style=plastic)](https://github.com/jacobwilliams/NumDiff/releases/latest)
 ![CI Status](https://github.com/jacobwilliams/NumDiff/actions/workflows/CI.yml/badge.svg)
+[![codecov](https://codecov.io/gh/jacobwilliams/NumDiff/branch/master/graph/badge.svg?token=43HK33CSMY)](https://codecov.io/gh/jacobwilliams/NumDiff)
 
 This is currently a work in progress. The goal is a comprehensive library that contains a full suite of computationally efficient implementations of algorithms for sparsity determination and numerical differentiation. This code is hosted on GitHub at: https://github.com/jacobwilliams/NumDiff
 
@@ -46,42 +48,48 @@ This is currently a work in progress. The goal is a comprehensive library that c
 
 ### FPM
 
-A `fmp.toml` file is provided for compiling roots-fortran with the [Fortran Package Manager](https://github.com/fortran-lang/fpm). For example, to build:
+A [Fortran Package Manager](https://github.com/fortran-lang/fpm) manifest file is included, so that the library and tests cases can be compiled with FPM. For example:
 
 ```
-  fpm build --profile release
+fpm build --profile release
+fpm test --profile release
 ```
 
-And to run the unit tests:
-
-```
-  fpm test
+To use `NumDiff` within your FPM project, add the following to your `fpm.toml` file:
+```toml
+[dependencies]
+NumDiff = { git="https://github.com/jacobwilliams/NumDiff.git" }
 ```
 
-### FoBiS
+To generate the documentation using [FORD](https://github.com/Fortran-FOSS-Programmers/ford), run:
 
-A [FoBiS](https://github.com/szaghi/FoBiS) configuration file (`numdiff.fobis`) is also provided that can also build the library and examples. Use the `mode` flag to indicate what to build. For example:
+```
+  ford numdiff.md
+```
 
-  * To build all the examples using gfortran: `FoBiS.py build -f numdiff.fobis -mode tests-gnu`
-  * To build all the examples using ifort: `FoBiS.py build -f numdiff.fobis -mode tests-intel`
-  * To build a static library using gfortran: `FoBiS.py build -f numdiff.fobis -mode static-gnu`
-  * To build a static library using ifort: `FoBiS.py build -f numdiff.fobis -mode static-intel`
+By default, the library is built with double precision (`real64`) real values. Explicitly specifying the real kind can be done using the following processor flags:
 
-  The full set of modes are: `static-gnu`, `static-gnu-debug`, `static-intel`, `static-intel-debug`, `shared-gnu`, `shared-gnu-debug`, `shared-intel`, `shared-intel-debug`, `tests-gnu`, `tests-gnu-debug`, `tests-intel`, `tests-intel-debug`
+Preprocessor flag | Kind  | Number of bytes
+----------------- | ----- | ---------------
+`REAL32`  | `real(kind=real32)`  | 4
+`REAL64`  | `real(kind=real64)`  | 8
+`REAL128` | `real(kind=real128)` | 16
 
-  To generate the documentation using [ford](https://github.com/Fortran-FOSS-Programmers/ford), run: ```FoBis.py rule --execute makedoc -f numdiff.fobis```
+For example, to build a single precision version of the library, use:
 
-  To run the test programs, run: ```FoBis.py rule --execute tests -f numdiff.fobis```
+```
+fpm build --profile release --flag "-DREAL32"
+```
 
 ## Documentation
 
-The latest API documentation can be found [here](http://jacobwilliams.github.io/NumDiff/). This was generated from the source code using [FORD](https://github.com/Fortran-FOSS-Programmers/ford) (note that the included `build.sh` script will also generate these files).
+The latest API documentation can be found [here](https://jacobwilliams.github.io/NumDiff/). This was generated from the source code using [FORD](https://github.com/Fortran-FOSS-Programmers/ford) (note that the included `build.sh` script will also generate these files).
 
 ## License
 
 The NumDiff source code and related files and documentation are distributed under a permissive free software [license](https://github.com/jacobwilliams/NumDiff/blob/master/LICENSE) (BSD-style).
 
 ## References
 
- * J. Oliver, "An algorithm for numerical differentiation of a function of one real variable", Journal of Computational and Applied Mathematics 6 (2) (1980) 145–160.  Fortran 77 code from [NIST](ftp://math.nist.gov/pub/repository/diff/src/DIFF)
+ * J. Oliver, "An algorithm for numerical differentiation of a function of one real variable", Journal of Computational and Applied Mathematics 6 (2) (1980) 145-160.  Fortran 77 code from [NIST](ftp://math.nist.gov/pub/repository/diff/src/DIFF)
  * Thomas F. Coleman, Burton S. Garbow, Jorge J. More, "Algorithm 618: FORTRAN subroutines for estimating sparse Jacobian Matrices", ACM Transactions on Mathematical Software (TOMS), Volume 10 Issue 3, Sept. 1984, Pages 346-347

build.sh

@@ -0,0 +1,13 @@
+comment:
+  layout: header, changes, diff, sunburst
+coverage:
+  ignore:
+  - test
+  - doc
+  status:
+    patch:
+      default:
+        target: 20%
+    project:
+      default:
+        target: 60%

codecov.yml

@@ -2,7 +2,7 @@ name = "NumDiff"
 version = "1.5.1"
 author = "Jacob Williams"
 maintainer = "Jacob Williams"
-copyright = "Copyright (c) 2016-2021, Jacob Williams"
+copyright = "Copyright (c) 2016-2022, Jacob Williams"
 license = "BSD-3"
 description = "Modern Fortran Numerical Differentiation Library"
 homepage = "https://github.com/jacobwilliams/NumDiff"