Merge pull request #31 from HaoZeke/fixupHeaders

ENH: Fixup headers, add single file exporter

.gitignore

@@ -1,6 +1,7 @@
 # Added
 /subprojects/*
 !/subprojects/*.wrap
+dist/
 
 # Created by https://www.toptal.com/developers/gitignore/api/fortran
 # Edit at https://www.toptal.com/developers/gitignore?templates=fortran

interfaces/CInterface/GaussJacobiQuadCInterp.c

@@ -1,3 +1,21 @@
+// BEGIN_HEADER
+// -----------------------------------------------------------------------------
+// Gauss-Jacobi Quadrature Implementation
+// Authors: Rohit Goswami <rgoswami[at]ieee.org>
+// Source: GaussJacobiQuad Library
+// License: MIT
+// GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
+// Date: 2023-08-28
+// Commit: c442f77
+// -----------------------------------------------------------------------------
+// This code is part of the GaussJacobiQuad library, providing an efficient
+// implementation for Gauss-Jacobi quadrature nodes and weights computation.
+// -----------------------------------------------------------------------------
+// To cite this software:
+// Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+// Zenodo: https://doi.org/10.5281/ZENODO.8285112
+// ---------------------------------------------------------------------
+// END_HEADER
 #include "GaussJacobiQuadCInterp.h"
 
 void gauss_jacobi_c(int* npts, double* alpha, double* beta, double x[], double wts[], const char* method) {

interfaces/CInterface/GaussJacobiQuadCInterp.h

@@ -5,12 +5,16 @@
 // Source: GaussJacobiQuad Library
 // License: MIT
 // GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
-// Date: 2023-08-26
-// Commit: 5dd0ffe
+// Date: 2023-08-28
+// Commit: c442f77
 // -----------------------------------------------------------------------------
 // This code is part of the GaussJacobiQuad library, providing an efficient
 // implementation for Gauss-Jacobi quadrature nodes and weights computation.
 // -----------------------------------------------------------------------------
+// To cite this software:
+// Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+// Zenodo: https://doi.org/10.5281/ZENODO.8285112
+// ---------------------------------------------------------------------
 // END_HEADER
 #ifndef GAUSSJACOBIQUADCINTERP_H
 #define GAUSSJACOBIQUADCINTERP_H

interfaces/CInterface/c_cli_gjpq.c

@@ -5,12 +5,16 @@
 // Source: GaussJacobiQuad Library
 // License: MIT
 // GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
-// Date: 2023-08-26
-// Commit: 5dd0ffe
+// Date: 2023-08-28
+// Commit: c442f77
 // -----------------------------------------------------------------------------
 // This code is part of the GaussJacobiQuad library, providing an efficient
 // implementation for Gauss-Jacobi quadrature nodes and weights computation.
 // -----------------------------------------------------------------------------
+// To cite this software:
+// Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+// Zenodo: https://doi.org/10.5281/ZENODO.8285112
+// ---------------------------------------------------------------------
 // END_HEADER
 #include <stdio.h>
 #include <stdlib.h>

interfaces/PyInterface/gjquad_cli.py

@@ -5,12 +5,16 @@
 # Source: GaussJacobiQuad Library
 # License: MIT
 # GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
-# Date: 2023-08-26
-# Commit: 5dd0ffe
+# Date: 2023-08-28
+# Commit: c442f77
 # -----------------------------------------------------------------------------
 # This code is part of the GaussJacobiQuad library, providing an efficient
 # implementation for Gauss-Jacobi quadrature nodes and weights computation.
 # -----------------------------------------------------------------------------
+# To cite this software:
+# Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+# Zenodo: https://doi.org/10.5281/ZENODO.8285112
+# ---------------------------------------------------------------------
 # END_HEADER
 """!
 @brief This script computes Gauss-Jacobi quadrature roots and weights using

newsfragments/10.explib.md

@@ -0,0 +1 @@
+Added a single file exporter for external libraries, which concatenates required files into one and updates the headers accordingly.

newsfragments/7.algo665.feature.md

@@ -1,3 +1,2 @@
-
 Added a variant of algorithm 665, refactored into gjp_common to
 accentuate similarities between 665 and standard GW

readme.org

@@ -33,6 +33,17 @@ meson compile -C bbdir
 ./bbdir/gjp_quad <npoints> <alpha> <beta> <method>
 #+end_src
 
+*** External Fortran libaries
+We support and encourage users to generate single file versions of the algorithms here to include in their code bases. This can be done with the ~scripts/add_headers.py~ script:
+#+begin_src bash
+# Strips comments by default
+python scripts/export_single.py --modulename "gjp_algo665"
+python scripts/export_single.py --modulename "gjp_gw" --keep-comments
+#+end_src
+These can be dropped into any code base or compiled as is into a shared library.
+#+begin_src bash
+gfortran dist/gjp_algo665_single.f90 --shared -fPIC -o libgjp_algo665.so
+#+end_src
 *** Interfaces
 *** C/C++ header interface
 We provide a header only interface, which bypasses passing strings between

scripts/add_headers.py

@@ -31,6 +31,10 @@
 {{cchar}} This code is part of the {{library_name}} library, providing an efficient
 {{cchar}} implementation for Gauss-Jacobi quadrature nodes and weights computation.
 {{cchar}} -----------------------------------------------------------------------------
+{{cchar}} To cite this software:
+{{cchar}} Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+{{cchar}} Zenodo: https://doi.org/10.5281/ZENODO.8285112
+{{cchar}} ---------------------------------------------------------------------
 {{cchar}} END_HEADER
 
 """
@@ -83,19 +87,19 @@ def add_headers(
         print("Headers added or updated in all files in" f" {directory} using {cchar}.")
 
 
-# Command-line arguments
-parser = argparse.ArgumentParser(description="Add headers to source files.")
-parser.add_argument(
-    "--dirs", type=str, required=True, nargs="+", help="Directory(s) to process"
-)
-parser.add_argument(
-    "--ftypes",
-    type=str,
-    required=True,
-    help="Comma-separated list of file types to process",
-)
-parser.add_argument("--cchar", type=str, required=True, help="Comment character")
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Add headers to source files.")
+    parser.add_argument(
+        "--dirs", type=str, required=True, nargs="+", help="Directory(s) to process"
+    )
+    parser.add_argument(
+        "--ftypes",
+        type=str,
+        required=True,
+        help="Comma-separated list of file types to process",
+    )
+    parser.add_argument("--cchar", type=str, required=True, help="Comment character")
 
-args = parser.parse_args()
-file_types = args.ftypes.split(",")
-add_headers(args.dirs, file_types, args.cchar)
+    args = parser.parse_args()
+    file_types = args.ftypes.split(",")
+    add_headers(args.dirs, file_types, args.cchar)

scripts/export_single.py

@@ -0,0 +1,83 @@
+#!/usr/bin/env python3
+# Cannot use ! in statements with this if strip-comments is true
+
+import argparse
+import os
+import re
+import subprocess
+from pathlib import Path
+
+import add_headers
+import fortdepend
+
+
+def get_git_root():
+    try:
+        git_root = (
+            subprocess.check_output(["git", "rev-parse", "--show-toplevel"])
+            .strip()
+            .decode("utf-8")
+        )
+        return Path(git_root)
+    except subprocess.CalledProcessError:
+        print("This directory is not part of a Git repository.")
+        return None
+
+
+def process_files(fname, strip_comments=True):
+    with open(fname, "r") as f:
+        content = f.read()
+    # Remove everything between ! BEGIN_HEADER and ! END_HEADER
+    content = re.sub(r"! BEGIN_HEADER.*?! END_HEADER\n", "", content, flags=re.DOTALL)
+    # Optionally, remove lines starting with !
+    if strip_comments:
+        content = re.sub(r"(!.*?$)|(\s*!.*?$)", "", content, flags=re.MULTILINE)
+    return content
+
+
+def export_single(modulename, strip_comments=True, outname=None):
+    if outname is None:
+        outname = f"{modulename}_single.f90"
+
+    prj_srcs = get_git_root() / "src"
+    os.chdir(prj_srcs)  # Needed for fortdepend
+
+    gaussjacobiquad = fortdepend.FortranProject()
+    concat_files = gaussjacobiquad.get_all_used_files(modulename)
+    print(f"Concatenating in reverse order {concat_files}")
+
+    exp_dat = []
+
+    for fname in reversed(concat_files):
+        processed_content = process_files(prj_srcs / fname, strip_comments)
+        exp_dat.append(processed_content)
+
+    with Path(get_git_root() / "dist" / outname).open("w") as f_out:
+        f_out.write("".join(exp_dat))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Export single file algorithms.")
+    parser.add_argument(
+        "--modulename", type=str, required=True, help="Module to export"
+    )
+    parser.add_argument(
+        "--outname", type=str, required=False, help="Defaults to modulename_single.f90"
+    )
+    parser.add_argument(
+        "--strip-comments",
+        dest="strip_comments",
+        action="store_true",
+        help="Remove comments",
+    )
+    parser.add_argument(
+        "--keep-comments",
+        dest="strip_comments",
+        action="store_false",
+        help="Keep comments",
+    )
+    parser.set_defaults(strip_comments=True)
+
+    args = parser.parse_args()
+    export_single(args.modulename, args.strip_comments, args.outname)
+    add_headers.add_headers([get_git_root() / "dist"], ["f90"])

scripts/scipy_gauss_jac.py

@@ -5,12 +5,16 @@
 # Source: GaussJacobiQuad Library
 # License: MIT
 # GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
-# Date: 2023-08-26
-# Commit: 5dd0ffe
+# Date: 2023-08-28
+# Commit: c442f77
 # -----------------------------------------------------------------------------
 # This code is part of the GaussJacobiQuad library, providing an efficient
 # implementation for Gauss-Jacobi quadrature nodes and weights computation.
 # -----------------------------------------------------------------------------
+# To cite this software:
+# Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+# Zenodo: https://doi.org/10.5281/ZENODO.8285112
+# ---------------------------------------------------------------------
 # END_HEADER
 """!
 @brief This script computes Gauss-Jacobi quadrature roots and weights using SymPy.

scripts/sympy_gauss_jac.py

@@ -5,12 +5,16 @@
 # Source: GaussJacobiQuad Library
 # License: MIT
 # GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
-# Date: 2023-08-26
-# Commit: 5dd0ffe
+# Date: 2023-08-28
+# Commit: c442f77
 # -----------------------------------------------------------------------------
 # This code is part of the GaussJacobiQuad library, providing an efficient
 # implementation for Gauss-Jacobi quadrature nodes and weights computation.
 # -----------------------------------------------------------------------------
+# To cite this software:
+# Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+# Zenodo: https://doi.org/10.5281/ZENODO.8285112
+# ---------------------------------------------------------------------
 # END_HEADER
 """!
 @brief This script computes Gauss-Jacobi quadrature roots and weights using SciPy.

src/GaussJacobiQuad.f90

@@ -6,11 +6,15 @@
 ! License: MIT
 ! GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
 ! Date: 2023-08-28
-! Commit: 69e8946
+! Commit: c442f77
 ! -----------------------------------------------------------------------------
 ! This code is part of the GaussJacobiQuad library, providing an efficient
 ! implementation for Gauss-Jacobi quadrature nodes and weights computation.
 ! -----------------------------------------------------------------------------
+! To cite this software:
+! Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+! Zenodo: https://doi.org/10.5281/ZENODO.8285112
+! ---------------------------------------------------------------------
 ! END_HEADER
 !> @brief Overall driver for Gauss-Jacobi quadrature.
 !
@@ -76,4 +80,4 @@ subroutine gauss_jacobi(npts, alpha, beta, x, wts, method)
     end select
 end subroutine gauss_jacobi
 
-end module
+end module GaussJacobiQuad

src/GaussJacobiQuadCCompat.f90

@@ -6,11 +6,15 @@
 ! License: MIT
 ! GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
 ! Date: 2023-08-28
-! Commit: 69e8946
+! Commit: c442f77
 ! -----------------------------------------------------------------------------
 ! This code is part of the GaussJacobiQuad library, providing an efficient
 ! implementation for Gauss-Jacobi quadrature nodes and weights computation.
 ! -----------------------------------------------------------------------------
+! To cite this software:
+! Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+! Zenodo: https://doi.org/10.5281/ZENODO.8285112
+! ---------------------------------------------------------------------
 ! END_HEADER
 !> @brief Compatibility layer for Gauss-Jacobi quadrature with C bindings.
 !

src/gjp_algo665.f90

@@ -6,11 +6,15 @@
 ! License: MIT
 ! GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
 ! Date: 2023-08-28
-! Commit: 69e8946
+! Commit: c442f77
 ! -----------------------------------------------------------------------------
 ! This code is part of the GaussJacobiQuad library, providing an efficient
 ! implementation for Gauss-Jacobi quadrature nodes and weights computation.
 ! -----------------------------------------------------------------------------
+! To cite this software:
+! Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+! Zenodo: https://doi.org/10.5281/ZENODO.8285112
+! ---------------------------------------------------------------------
 ! END_HEADER
 !> @brief This module provides routines for numerical integration using Gauss-Jacobi quadrature.
 !! @details The implementation is based on the GW method as implemented in the GaussJacobiQuad

src/gjp_common.f90

@@ -6,11 +6,15 @@
 ! License: MIT
 ! GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
 ! Date: 2023-08-28
-! Commit: 69e8946
+! Commit: c442f77
 ! -----------------------------------------------------------------------------
 ! This code is part of the GaussJacobiQuad library, providing an efficient
 ! implementation for Gauss-Jacobi quadrature nodes and weights computation.
 ! -----------------------------------------------------------------------------
+! To cite this software:
+! Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+! Zenodo: https://doi.org/10.5281/ZENODO.8285112
+! ---------------------------------------------------------------------
 ! END_HEADER
 !> @brief This module provides utility functions for computing Jacobi matrices and zeroth moments.
 !!

src/gjp_constants.f90

@@ -6,11 +6,15 @@
 ! License: MIT
 ! GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
 ! Date: 2023-08-28
-! Commit: 69e8946
+! Commit: c442f77
 ! -----------------------------------------------------------------------------
 ! This code is part of the GaussJacobiQuad library, providing an efficient
 ! implementation for Gauss-Jacobi quadrature nodes and weights computation.
 ! -----------------------------------------------------------------------------
+! To cite this software:
+! Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+! Zenodo: https://doi.org/10.5281/ZENODO.8285112
+! ---------------------------------------------------------------------
 ! END_HEADER
 !> @brief Constants contain more digits than double precision, so that
 !> they are rounded correctly.
@@ -41,4 +45,4 @@ module gjp_constants
 real(dp), parameter :: c_2002 = 137.03599911_dp
 real(dp), parameter :: c_1998 = 137.03599976_dp
 real(dp), parameter :: c_1986 = 137.0359895_dp ! To compare with dftatom
-end module
+end module gjp_constants

src/gjp_gw.f90

@@ -6,11 +6,15 @@
 ! License: MIT
 ! GitHub Repository: https://github.com/HaoZeke/GaussJacobiQuad
 ! Date: 2023-08-28
-! Commit: 69e8946
+! Commit: c442f77
 ! -----------------------------------------------------------------------------
 ! This code is part of the GaussJacobiQuad library, providing an efficient
 ! implementation for Gauss-Jacobi quadrature nodes and weights computation.
 ! -----------------------------------------------------------------------------
+! To cite this software:
+! Rohit Goswami (2023). HaoZeke/GaussJacobiQuad: v0.1.0.
+! Zenodo: https://doi.org/10.5281/ZENODO.8285112
+! ---------------------------------------------------------------------
 ! END_HEADER
 !> @brief Module for computing Gauss-Jacobi quadrature nodes and weights using the Golub-Welsch (GW) method
 !> @details The implementation is based on the Golub-Welsch method as used in chebfun (https://chebfun.org) and references: