16 code review

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.gitignore

@@ -45,4 +45,9 @@ x64
 
 # test artifacts:
 /*.pdf
-/*.py
+/*.py
+/coverage
+
+# pixi environments
+.pixi/*
+!.pixi/config.toml

LICENSE

@@ -1,7 +1,7 @@
 NumDiff -- Numerical Differentiation Library
 https://github.com/jacobwilliams/NumDiff
 
-Copyright (c) 2016-2022, Jacob Williams
+Copyright (c) 2016-2026, Jacob Williams
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

coverage.sh

@@ -0,0 +1,67 @@
+#!/bin/bash
+# Script to run tests with coverage and generate reports
+
+set -e
+
+COV_DIR="coverage"
+
+# Find the correct gcov (matching gfortran version)
+GCOV=$(dirname $(which gfortran))/gcov
+
+echo "Using gcov: $GCOV"
+echo ""
+echo "================================================"
+echo "Running tests with coverage..."
+echo "================================================"
+
+# Clear the execution counts of any previous run (so they don't accumulate)
+find build -name "*.gcda" -delete 2>/dev/null || true
+
+# Build and run tests with coverage flags
+fpm test --flag "--coverage"
+
+echo ""
+echo "================================================"
+echo "Generating coverage report with lcov..."
+echo "================================================"
+
+# Create a fresh coverage directory and copy the build artifacts into it. Only
+# from the build just made: older coverage builds (with a different build-flag
+# hash, e.g. after an fpm.toml change) hold stale data for the same files.
+LATEST_GCNO=$(ls -t build/gfortran_*/*/*.gcno | head -1)
+BUILD_DIR=$(dirname "$(dirname "$LATEST_GCNO")")
+echo "Using build directory: $BUILD_DIR"
+rm -rf "$COV_DIR"
+mkdir -p "$COV_DIR"
+cp -r "$BUILD_DIR"/*/* "$COV_DIR/" 2>/dev/null || true
+# don't show coverage of test/examples programs:
+rm -rf "$COV_DIR"/test_*
+rm -rf "$COV_DIR"/example_*
+# we want to skip the files that start with 'build_dependencies' because they are not part of the source code
+find "$COV_DIR" -name "build_dependencies*" -exec rm -rf {} +
+
+# Capture initial coverage (baseline)
+lcov --ignore-errors inconsistent --gcov-tool "$GCOV" --capture --initial --base-directory . --directory "$COV_DIR" --output-file "$COV_DIR/coverage.base" --quiet
+
+# Capture test execution coverage
+lcov --ignore-errors inconsistent --gcov-tool "$GCOV" --capture --base-directory . --directory "$COV_DIR" --output-file "$COV_DIR/coverage.capture" --quiet
+
+# Combine baseline and test coverage
+lcov --add-tracefile "$COV_DIR/coverage.base" --add-tracefile "$COV_DIR/coverage.capture" --output-file "$COV_DIR/coverage.info" --quiet
+
+echo ""
+echo "================================================"
+echo "Coverage Summary"
+echo "================================================"
+
+# Display summary
+lcov --summary "$COV_DIR/coverage.info"
+
+echo ""
+echo "Coverage data saved to: $COV_DIR/coverage.info"
+echo ""
+echo "generate HTML report:"
+
+genhtml $COV_DIR/coverage.info --output-directory $COV_DIR/html --dark-mode
+
+echo ""

fpm.toml

@@ -1,8 +1,8 @@
 name = "NumDiff"
-version = "1.5.1"
+version = "1.8.2"
 author = "Jacob Williams"
 maintainer = "Jacob Williams"
-copyright = "Copyright (c) 2016-2022, Jacob Williams"
+copyright = "Copyright (c) 2016-2026, Jacob Williams"
 license = "BSD-3"
 description = "Modern Fortran Numerical Differentiation Library"
 homepage = "https://github.com/jacobwilliams/NumDiff"
@@ -14,24 +14,9 @@ source-dir = "src"
 library = true
 
 [build]
-auto-executables = false
-auto-examples = false
-auto-tests = false
+auto-executables = true
+auto-examples = true
+auto-tests = true
 
 [dev-dependencies]
 pyplot-fortran = { git="https://github.com/jacobwilliams/pyplot-fortran.git", tag = "3.2.1" }
-
-[[test]]
-name = "dsm_test"
-source-dir = "tests"
-main = "dsm_test.f90"
-
-[[test]]
-name = "test1"
-source-dir = "tests"
-main = "test1.f90"
-
-[[test]]
-name = "test2"
-source-dir = "tests"
-main = "test2.f90"

pixi.toml

@@ -0,0 +1,17 @@
+[workspace]
+authors = ["Jacob Williams <jacobwilliams@users.noreply.github.com>"]
+channels = ["conda-forge"]
+name = "NumDiff"
+platforms = ["osx-arm64"]
+version = "1.8.2"
+
+[tasks]
+
+[dependencies]
+gfortran = "15.*"
+fpm = ">=0.13.0,<0.14"
+python = ">=3.14.7,<3.15"
+graphviz = ">=14.1.2,<15"
+ford = ">=7.0.13,<8"
+matplotlib = ">=3.11.2,<4"
+lcov = ">=2.5,<3"

src/cache_module.f90

@@ -70,7 +70,7 @@ subroutine initialize_cache(me,isize,n,m,chunk_size)
     me%m = m
 
     if (present(chunk_size)) then
-        me%chunk_size = chunk_size
+        me%chunk_size = max(1,chunk_size)
     else
         me%chunk_size = 100
     end if
@@ -95,7 +95,7 @@ subroutine print_cache(me,iunit)
     write(iunit,'(A)') ''
     write(iunit,'(A)') '------------------------'
     if (allocated(me%c)) then
-        do i = 1, size(me%c)
+        do i = lbound(me%c,1), ubound(me%c,1)  ! note: the table is 0-based
             if (allocated(me%c(i)%x)) then
                 write(iunit,'(A)') ''
                 write(iunit,'(A,1X,I10)') 'Entry ',i

src/dsm_module.f90

@@ -94,9 +94,11 @@ subroutine dsm(m,n,Npairs,Indrow,Indcol,Ngrp,Maxgrp,Mingrp,Info,Ipntr,Jpntr)
                                                     !! note that `jpntr(n+1)-1` is then the number of non-zero
                                                     !! elements of the matrix `a`.
 
-    integer,dimension(max(m,6*n)) :: iwa     !! an integer work array
+    integer,dimension(:),allocatable :: iwa !! an integer work array
     integer :: i , ir , j , jp , k , maxclq , nnz , numgrp
 
+    allocate(iwa(max(m,6*n)))
+
     !  check the input data.
 
     Info = 0
@@ -395,7 +397,9 @@ subroutine ido(m,n,Indrow,Jpntr,Indcol,Ipntr,Ndeg,List,Maxclq, &
     do ir = 1 , m
         maxlst = maxlst + (Ipntr(ir+1)-Ipntr(ir))**2
     enddo
-    maxlst = maxlst/n
+    ! at least one column must be examined, otherwise
+    ! jcol would not be set in the selection loop below:
+    maxlst = max(1,maxlst/n)
     Maxclq = 0
     numord = 1