Fix missing import in finiterectlat-scatter.py

Stupid typo with possibly serious consequences...

.drone.yml

@@ -0,0 +1,83 @@
+---
+kind: pipeline
+type: docker
+name: buildqpms-alpine-preinstlibs
+
+workspace:
+  path: /home/qpmsbuild/qpms
+
+# don't run in master until the python/lapacke linking problem is resolved
+trigger:
+  branch:
+    exclude: 
+      - master
+
+steps:
+- name: chown
+  image: qpms/buildenv/alpine/pkgdnumlib
+  pull: never
+  commands:
+    - chown -R qpmsbuild.qpmsbuild .
+- name: submodules
+  image: qpms/buildenv/alpine/pkgdnumlib
+  pull: never
+  user: qpmsbuild
+  commands:
+    - git submodule init
+    - git submodule update
+- name: build
+  image: qpms/buildenv/alpine/pkgdnumlib
+  pull: never
+  user: qpmsbuild
+  commands:
+  - cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local .
+  - make install
+  - export LIBRARY_PATH=$HOME/.local/lib
+  - python3 setup.py install --user
+  - cd examples/rectangular/modes
+  - pip3 install --user matplotlib #needed to run the example
+  - export LD_LIBRARY_PATH=$HOME/.local/lib
+  - ./01a_realfreq_svd.sh
+
+---
+kind: pipeline
+type: docker
+name: buildqpms-debian-preinstlibs
+
+workspace:
+  path: /home/qpmsbuild/qpms
+
+steps:
+- name: chown
+  image: qpms/buildenv/debian/pkgdnumlib
+  pull: never
+  commands:
+    - chown -R qpmsbuild.qpmsbuild .
+- name: submodules
+  image: qpms/buildenv/debian/pkgdnumlib
+  pull: never
+  user: qpmsbuild
+  commands:
+    - git submodule init
+    - git submodule update
+- name: build
+  image: qpms/buildenv/debian/pkgdnumlib
+  pull: never
+  user: qpmsbuild
+  commands:
+  - cmake -DCMAKE_INSTALL_PREFIX=/home/qpmsbuild/.local .
+  - make install
+  - export LIBRARY_PATH=$HOME/.local/lib
+  - python3 setup.py install --user
+  - pip3 install --user matplotlib #needed to run the examples
+  - export LD_LIBRARY_PATH=$HOME/.local/lib
+  - cd examples/rectangular/modes
+  - ./01a_realfreq_svd.sh
+  - cd -
+  - cd examples/hexagonal/modes
+  #- ./01a_realfreq_svd.sh 
+  #- ./01_compute_modes.sh 
+  #- ./02b_compute_disp_0M.sh 
+  #- ./02_compute_disp.sh 
+  #- ./02x_compute_disp.sh
+

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "camos"]
 	path = camos
-	url = https://github.com/texnokrates/zbessel.git
+	url = https://codeberg.org/QPMS/zbessel.git
 	branch = purec

CMakeLists.txt

@@ -10,7 +10,7 @@ include(GNUInstallDirs)
 
 project (QPMS)
 
-
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/")
 
 macro(use_c99)
   if (CMAKE_VERSION VERSION_LESS "3.1")

Doxyfile

@@ -753,7 +753,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = qpms notes misc finite_systems.md CLIUTILS.md README.md README.Triton.md finite_systems.md lattices.md TODO.md
+INPUT                  = qpms notes misc finite_systems.md MIRRORS.md CLIUTILS.md README.md README.Triton.md finite_systems.md lattices.md TODO.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

MIRRORS.md

@@ -0,0 +1,14 @@
+QPMS source code mirrors
+========================
+
+QPMS source code is available at several locations; in all of the following,
+upstream `master` branch is kept up-to-date. Various development branches
+are not necessarily pushed everywhere (and they should be considered
+unstable in the sense that rebases and forced pushes are possible).
+
+mirror                                          | note                    | provider                                          | backend
+----------------------------------------------- | ----------------------- | ------------------------------------------------- | ------
+<https://repo.or.cz/qpms.git>                   | primary public upstream | [repo.or.cz](https://repo.or.cz/)                 | girocco
+<https://codeberg.org/QPMS/qpms>                |                         | [Codeberg](https://codeberg.org)                  | gitea
+<https://git.piraattipuolue.fi/QPMS/qpms.git>   |                         | [Pirate Party Finland](https://piraattipuolue.fi) | gitea
+<https://version.aalto.fi/gitlab/qpms/qpms.git> |                         | [Aalto University](https://aalto.fi)              | gitlab 

README.md

@@ -1,7 +1,9 @@
+[![Build Status](https://drone.perkele.eu/api/badges/QPMS/qpms/status.svg)](https://drone.perkele.eu/QPMS/qpms)
+
 QPMS README
 ===========
 
-QPMS (standing for QPMS Photonic Multiple Scattering) 
+[QPMS][homepage] (standing for QPMS Photonic Multiple Scattering) 
 is a toolkit for frequency-domain simulations of photonic systems
 consisting of compact objects (particles) inside a homogeneous medium. Scattering
 properties of the individual particles are described by their T-matrices
@@ -43,7 +45,8 @@ Infinite systems (lattices)
 Getting the code
 ================
 
-The main upstream public repository is located at <https://repo.or.cz/qpms.git>.
+The codebase is available at the main upstream public repository
+<https://repo.or.cz/qpms.git> or any of the [maintained mirrors][MIRRORS].
 Just clone the repository with `git` and proceed to the installation instructions
 below.
 
@@ -89,14 +92,21 @@ Special care might need to be taken when installing QPMS in cluster environments
 Specific installation instructions for Aalto University's Triton cluster
 can be found in a [separate document][TRITON-README].
 
+Instructions for installation on Android-based devices are
+in [another document][INSTALL-ANDROID].
+
 
 Documentation
 =============
 
-Documentation of QPMS is a work in progress. Most of the newer code
-is documented using [doxygen][] comments. To build the documentation, just run
+[QPMS documentation][homepage] is a work in progress. Most of the newer code
+is documented using [doxygen][] comments. Documentation generated for the
+upstream version is hosted on the QPMS homepage <https://qpms.necada.org>.
+
+To build the documentation yourself, 
+just run
 `doxygen`
-in the root directory; the documentation will then be found in 
+in the QPMS source root directory; the documentation will then be found in 
 `docs/html/index.html`.
 
 Of course, the prerequisite of this is having doxygen installed.
@@ -166,12 +176,13 @@ You are also warmly welcome to the [QPMS user chat][telegramchat]
 in Telegram!
 
 
-
+[homepage]: https://qpms.necada.org
 [SCUFF-EM]: https://homerreid.github.io/scuff-em-documentation/
 [OpenBLAS]: https://www.openblas.net/
 [GSL]: https://www.gnu.org/software/gsl/
 [cmake]: https://cmake.org
 [TRITON-README]: README.Triton.md
+[INSTALL-ANDROID]: notes/INSTALL_ANDROID.md
 [tutorial-finite]: finite_systems.md
 [tutorial-infinite]: lattices.md
 [doxygen]: http://doxygen.nl/
@@ -180,3 +191,4 @@ in Telegram!
 [telegramchat]: https://t.me/QPMScattering
 [authormail]: mailto:marek@necada.org
 [cliutils]: CLIUTILS.md
+[MIRRORS]: MIRRORS.md

ci/00_make_dockerfiles.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+DP=Dockerfile_parts
+# "Build environment" Dockerfiles
+cat >Dockerfile.benv.debian.bnl ${DP}/00_common.debian ${DP}/01_numlibs.built
+cat >Dockerfile.benv.debian.pnl ${DP}/00_common.debian ${DP}/01_numlibs.debian.pkgd
+cat >Dockerfile.benv.alpine.bnl ${DP}/00_common.alpine ${DP}/01_numlibs.built
+cat >Dockerfile.benv.alpine.pnl ${DP}/00_common.alpine ${DP}/01_numlibs.alpine.pkgd

ci/01_make_buildenv_images.sh

@@ -0,0 +1,5 @@
+#!/bin/sh
+docker build -t qpms/buildenv/debian/builtnumlib -f Dockerfile.benv.debian.bnl .
+docker build -t qpms/buildenv/debian/pkgdnumlib -f Dockerfile.benv.debian.pnl .
+docker build -t qpms/buildenv/alpine/builtnumlib -f Dockerfile.benv.alpine.bnl .
+docker build -t qpms/buildenv/alpine/pkgdnumlib -f Dockerfile.benv.alpine.pnl .

ci/Dockerfile_parts/00_common.alpine

@@ -0,0 +1,5 @@
+FROM alpine:latest AS commondeps
+RUN apk update \
+ && apk add cmake python3-dev py3-pip gcc g++ wget git make libc-dev bc \
+ && adduser -D qpmsbuild
+

ci/Dockerfile_parts/00_common.debian

@@ -0,0 +1,6 @@
+FROM debian:stable AS commondeps
+RUN apt-get update \
+ && apt-get -y install --no-install-recommends build-essential cmake python3 python3-pip git wget python3-dev bc \
+ && apt-get clean \
+ && useradd -m qpmsbuild
+

ci/Dockerfile_parts/01_numlibs.alpine.pkgd

@@ -0,0 +1,3 @@
+FROM commondeps AS numlibs
+# openblas-dev adds gfortran :(
+RUN apk add openblas-dev gsl-dev

ci/Dockerfile_parts/01_numlibs.built

@@ -0,0 +1,16 @@
+FROM commondeps AS buildopenblas
+USER qpmsbuild
+RUN cd && git clone --depth 1 https://github.com/xianyi/OpenBLAS.git \
+ && cd OpenBLAS && make \
+ && make install PREFIX=$HOME/.local/ \
+ && make clean \
+ && cd .. && rm -rf OpenBLAS
+
+FROM buildopenblas AS numlibs
+USER qpmsbuild
+RUN cd && wget https://ftp.gnu.org/gnu/gsl/gsl-latest.tar.gz \
+ && tar xf gsl-latest.tar.gz \
+ && cd $( tar tf gsl-latest.tar.gz | head -n 1 ) \
+ && ./configure --prefix=$HOME/.local \
+ && make && make install && make clean \
+ && cd .. && rm -rf $OLDPWD gsl-latest.tar.gz

ci/Dockerfile_parts/01_numlibs.debian.pkgd

@@ -0,0 +1,4 @@
+FROM commondeps AS numlibs
+RUN apt-get -y install --no-install-recommends libopenblas-dev libgsl-dev liblapacke-dev \
+ && apt-get clean
+

ci/Dockerfile_parts/02_buildqpms

@@ -0,0 +1,12 @@
+FROM numlibs AS buildqpms
+USER qpmsbuild
+ENV LD_LIBRARY_PATH /home/qpmsbuild/.local/lib
+ENV LIBRARY_PATH /home/qpmsbuild/.local/lib
+ENV C_INCLUDE_PATH /home/qpmsbuild/.local/include
+RUN cd && git clone --depth 1 https://repo.or.cz/qpms.git \
+ && cd qpms && git submodule init && git submodule update 
+RUN cd ~/qpms && cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local . \
+ && make \
+ && make install
+RUN cd ~/qpms && python3 setup.py install --user
+

ci/drone.yml

@@ -0,0 +1 @@
+../.drone.yml

cmake/GetGitRevisionDescription.cmake

@@ -0,0 +1,284 @@
+# - Returns a version string from Git
+#
+# These functions force a re-configure on each git commit so that you can
+# trust the values of the variables in your build system.
+#
+#  get_git_head_revision(<refspecvar> <hashvar> [ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR])
+#
+# Returns the refspec and sha hash of the current head revision
+#
+#  git_describe(<var> [<additional arguments to git describe> ...])
+#
+# Returns the results of git describe on the source tree, and adjusting
+# the output so that it tests false if an error occurs.
+#
+#  git_describe_working_tree(<var> [<additional arguments to git describe> ...])
+#
+# Returns the results of git describe on the working tree (--dirty option),
+# and adjusting the output so that it tests false if an error occurs.
+#
+#  git_get_exact_tag(<var> [<additional arguments to git describe> ...])
+#
+# Returns the results of git describe --exact-match on the source tree,
+# and adjusting the output so that it tests false if there was no exact
+# matching tag.
+#
+#  git_local_changes(<var>)
+#
+# Returns either "CLEAN" or "DIRTY" with respect to uncommitted changes.
+# Uses the return code of "git diff-index --quiet HEAD --".
+# Does not regard untracked files.
+#
+# Requires CMake 2.6 or newer (uses the 'function' command)
+#
+# Original Author:
+# 2009-2020 Ryan Pavlik <ryan.pavlik@gmail.com> <abiryan@ryand.net>
+# http://academic.cleardefinition.com
+#
+# Copyright 2009-2013, Iowa State University.
+# Copyright 2013-2020, Ryan Pavlik
+# Copyright 2013-2020, Contributors
+# SPDX-License-Identifier: BSL-1.0
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+
+if(__get_git_revision_description)
+    return()
+endif()
+set(__get_git_revision_description YES)
+
+# We must run the following at "include" time, not at function call time,
+# to find the path to this module rather than the path to a calling list file
+get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH)
+
+# Function _git_find_closest_git_dir finds the next closest .git directory
+# that is part of any directory in the path defined by _start_dir.
+# The result is returned in the parent scope variable whose name is passed
+# as variable _git_dir_var. If no .git directory can be found, the
+# function returns an empty string via _git_dir_var.
+#
+# Example: Given a path C:/bla/foo/bar and assuming C:/bla/.git exists and
+# neither foo nor bar contain a file/directory .git. This wil return
+# C:/bla/.git
+#
+function(_git_find_closest_git_dir _start_dir _git_dir_var)
+    set(cur_dir "${_start_dir}")
+    set(git_dir "${_start_dir}/.git")
+    while(NOT EXISTS "${git_dir}")
+        # .git dir not found, search parent directories
+        set(git_previous_parent "${cur_dir}")
+        get_filename_component(cur_dir "${cur_dir}" DIRECTORY)
+        if(cur_dir STREQUAL git_previous_parent)
+            # We have reached the root directory, we are not in git
+            set(${_git_dir_var}
+                ""
+                PARENT_SCOPE)
+            return()
+        endif()
+        set(git_dir "${cur_dir}/.git")
+    endwhile()
+    set(${_git_dir_var}
+        "${git_dir}"
+        PARENT_SCOPE)
+endfunction()
+
+function(get_git_head_revision _refspecvar _hashvar)
+    _git_find_closest_git_dir("${CMAKE_CURRENT_SOURCE_DIR}" GIT_DIR)
+
+    if("${ARGN}" STREQUAL "ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR")
+        set(ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR TRUE)
+    else()
+        set(ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR FALSE)
+    endif()
+    if(NOT "${GIT_DIR}" STREQUAL "")
+        file(RELATIVE_PATH _relative_to_source_dir "${CMAKE_SOURCE_DIR}"
+             "${GIT_DIR}")
+        if("${_relative_to_source_dir}" MATCHES "[.][.]" AND NOT ALLOW_LOOKING_ABOVE_CMAKE_SOURCE_DIR)
+            # We've gone above the CMake root dir.
+            set(GIT_DIR "")
+        endif()
+    endif()
+    if("${GIT_DIR}" STREQUAL "")
+        set(${_refspecvar}
+            "GITDIR-NOTFOUND"
+            PARENT_SCOPE)
+        set(${_hashvar}
+            "GITDIR-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+
+    # Check if the current source dir is a git submodule or a worktree.
+    # In both cases .git is a file instead of a directory.
+    #
+    if(NOT IS_DIRECTORY ${GIT_DIR})
+        # The following git command will return a non empty string that
+        # points to the super project working tree if the current
+        # source dir is inside a git submodule.
+        # Otherwise the command will return an empty string.
+        #
+        execute_process(
+            COMMAND "${GIT_EXECUTABLE}" rev-parse
+                    --show-superproject-working-tree
+            WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+            OUTPUT_VARIABLE out
+            ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+        if(NOT "${out}" STREQUAL "")
+            # If out is empty, GIT_DIR/CMAKE_CURRENT_SOURCE_DIR is in a submodule
+            file(READ ${GIT_DIR} submodule)
+            string(REGEX REPLACE "gitdir: (.*)$" "\\1" GIT_DIR_RELATIVE
+                                 ${submodule})
+            string(STRIP ${GIT_DIR_RELATIVE} GIT_DIR_RELATIVE)
+            get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH)
+            get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE}
+                                   ABSOLUTE)
+            set(HEAD_SOURCE_FILE "${GIT_DIR}/HEAD")
+        else()
+            # GIT_DIR/CMAKE_CURRENT_SOURCE_DIR is in a worktree
+            file(READ ${GIT_DIR} worktree_ref)
+            # The .git directory contains a path to the worktree information directory
+            # inside the parent git repo of the worktree.
+            #
+            string(REGEX REPLACE "gitdir: (.*)$" "\\1" git_worktree_dir
+                                 ${worktree_ref})
+            string(STRIP ${git_worktree_dir} git_worktree_dir)
+            _git_find_closest_git_dir("${git_worktree_dir}" GIT_DIR)
+            set(HEAD_SOURCE_FILE "${git_worktree_dir}/HEAD")
+        endif()
+    else()
+        set(HEAD_SOURCE_FILE "${GIT_DIR}/HEAD")
+    endif()
+    set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
+    if(NOT EXISTS "${GIT_DATA}")
+        file(MAKE_DIRECTORY "${GIT_DATA}")
+    endif()
+
+    if(NOT EXISTS "${HEAD_SOURCE_FILE}")
+        return()
+    endif()
+    set(HEAD_FILE "${GIT_DATA}/HEAD")
+    configure_file("${HEAD_SOURCE_FILE}" "${HEAD_FILE}" COPYONLY)
+
+    configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in"
+                   "${GIT_DATA}/grabRef.cmake" @ONLY)
+    include("${GIT_DATA}/grabRef.cmake")
+
+    set(${_refspecvar}
+        "${HEAD_REF}"
+        PARENT_SCOPE)
+    set(${_hashvar}
+        "${HEAD_HASH}"
+        PARENT_SCOPE)
+endfunction()
+
+function(git_describe _var)
+    if(NOT GIT_FOUND)
+        find_package(Git QUIET)
+    endif()
+    get_git_head_revision(refspec hash)
+    if(NOT GIT_FOUND)
+        set(${_var}
+            "GIT-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+    if(NOT hash)
+        set(${_var}
+            "HEAD-HASH-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+
+    # TODO sanitize
+    #if((${ARGN}" MATCHES "&&") OR
+    #	(ARGN MATCHES "||") OR
+    #	(ARGN MATCHES "\\;"))
+    #	message("Please report the following error to the project!")
+    #	message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
+    #endif()
+
+    #message(STATUS "Arguments to execute_process: ${ARGN}")
+
+    execute_process(
+        COMMAND "${GIT_EXECUTABLE}" describe --tags --always ${hash} ${ARGN}
+        WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+        RESULT_VARIABLE res
+        OUTPUT_VARIABLE out
+        ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(NOT res EQUAL 0)
+        set(out "${out}-${res}-NOTFOUND")
+    endif()
+
+    set(${_var}
+        "${out}"
+        PARENT_SCOPE)
+endfunction()
+
+function(git_describe_working_tree _var)
+    if(NOT GIT_FOUND)
+        find_package(Git QUIET)
+    endif()
+    if(NOT GIT_FOUND)
+        set(${_var}
+            "GIT-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+
+    execute_process(
+        COMMAND "${GIT_EXECUTABLE}" describe --dirty ${ARGN}
+        WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+        RESULT_VARIABLE res
+        OUTPUT_VARIABLE out
+        ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(NOT res EQUAL 0)
+        set(out "${out}-${res}-NOTFOUND")
+    endif()
+
+    set(${_var}
+        "${out}"
+        PARENT_SCOPE)
+endfunction()
+
+function(git_get_exact_tag _var)
+    git_describe(out --exact-match ${ARGN})
+    set(${_var}
+        "${out}"
+        PARENT_SCOPE)
+endfunction()
+
+function(git_local_changes _var)
+    if(NOT GIT_FOUND)
+        find_package(Git QUIET)
+    endif()
+    get_git_head_revision(refspec hash)
+    if(NOT GIT_FOUND)
+        set(${_var}
+            "GIT-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+    if(NOT hash)
+        set(${_var}
+            "HEAD-HASH-NOTFOUND"
+            PARENT_SCOPE)
+        return()
+    endif()
+
+    execute_process(
+        COMMAND "${GIT_EXECUTABLE}" diff-index --quiet HEAD --
+        WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+        RESULT_VARIABLE res
+        OUTPUT_VARIABLE out
+        ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(res EQUAL 0)
+        set(${_var}
+            "CLEAN"
+            PARENT_SCOPE)
+    else()
+        set(${_var}
+            "DIRTY"
+            PARENT_SCOPE)
+    endif()
+endfunction()

cmake/GetGitRevisionDescription.cmake.in

@@ -0,0 +1,43 @@
+#
+# Internal file for GetGitRevisionDescription.cmake
+#
+# Requires CMake 2.6 or newer (uses the 'function' command)
+#
+# Original Author:
+# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
+# http://academic.cleardefinition.com
+# Iowa State University HCI Graduate Program/VRAC
+#
+# Copyright 2009-2012, Iowa State University
+# Copyright 2011-2015, Contributors
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+# SPDX-License-Identifier: BSL-1.0
+
+set(HEAD_HASH)
+
+file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
+
+string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS)
+if(HEAD_CONTENTS MATCHES "ref")
+	# named branch
+	string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}")
+	if(EXISTS "@GIT_DIR@/${HEAD_REF}")
+		configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
+	else()
+		configure_file("@GIT_DIR@/packed-refs" "@GIT_DATA@/packed-refs" COPYONLY)
+		file(READ "@GIT_DATA@/packed-refs" PACKED_REFS)
+		if(${PACKED_REFS} MATCHES "([0-9a-z]*) ${HEAD_REF}")
+			set(HEAD_HASH "${CMAKE_MATCH_1}")
+		endif()
+	endif()
+else()
+	# detached HEAD
+	configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY)
+endif()
+
+if(NOT HEAD_HASH)
+	file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024)
+	string(STRIP "${HEAD_HASH}" HEAD_HASH)
+endif()

cmake/LICENSE_1_0.txt

@@ -0,0 +1,23 @@
+Boost Software License - Version 1.0 - August 17th, 2003
+
+Permission is hereby granted, free of charge, to any person or organization
+obtaining a copy of the software and accompanying documentation covered by
+this license (the "Software") to use, reproduce, display, distribute,
+execute, and transmit the Software, and to prepare derivative works of the
+Software, and to permit third-parties to whom the Software is furnished to
+do so, all subject to the following:
+
+The copyright notices in the Software and this entire statement, including
+the above license grant, this restriction and the following disclaimer,
+must be included in all copies of the Software, in whole or in part, and
+all derivative works of the Software, unless such copies or derivative
+works are solely in the form of machine-executable object code generated by
+a source language processor.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

misc/finiterectlat-constant-driving.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 import math
-from qpms.argproc import ArgParser, make_dict_action, sslice
+from qpms.argproc import ArgParser, make_dict_action, sslice, annotate_pdf_metadata
 figscale=3
 
 ap = ArgParser(['rectlattice2d_finite', 'single_particle', 'single_lMax', 'single_omega'])
@@ -44,7 +44,7 @@ import numpy as np
 import qpms
 from qpms.cybspec import BaseSpec
 from qpms.cytmatrices import CTMatrix, TMatrixGenerator
-from qpms.qpms_c import Particle
+from qpms.qpms_c import Particle, qpms_library_version
 from qpms.cymaterials import EpsMu, EpsMuGenerator, LorentzDrudeModel, lorentz_drude
 from qpms.cycommon import DebugFlags, dbgmsg_enable
 from qpms import FinitePointGroup, ScatteringSystem, BesselType, eV, hbar
@@ -225,7 +225,7 @@ for iri in range(ss.nirreps):
             scattered_full[spi, y] += scattered_ir_unpacked[spi, y]
     if a.save_gradually:
         iriout = outfile_tmp + ".%d" % iri
-        np.savez(iriout, iri=iri, meta=vars(a), 
+        np.savez(iriout, iri=iri, meta={**vars(a), 'qpms_version' : qpms.__version__()}, 
 		 omega=omega, wavenumber=wavenumber, nelem=nelem, wavevector=np.array(a.wavevector), phases=phases, 
                  positions = ss.positions[:,:2],
                  scattered_ir_packed = scattered_ir[iri], 
@@ -251,10 +251,10 @@ if not math.isnan(a.ccd_distance):
     logging.info("Far fields done")
 
 outfile = defaultprefix + ".npz" if a.output is None else a.output
-np.savez(outfile, meta=vars(a), 
+np.savez(outfile, meta={**vars(a), 'qpms_version' : qpms.__version__()}, 
 		 omega=omega, wavenumber=wavenumber, nelem=nelem, wavevector=np.array(a.wavevector), phases=phases, 
                  positions = ss.positions[:,:2],
-                 scattered_ir_packed = scattered_ir, 
+                 scattered_ir_packed = np.array(scattered_ir, dtype=np.object),
                  scattered_full = scattered_full,
                  ir_contained = ir_contained,
                  t=t, l=l, m=m,
@@ -355,6 +355,7 @@ if a.plot or (a.plot_out is not None):
                     axes[y,gg].yaxis.set_major_formatter(plt.NullFormatter())
         fig.text(0, 0, str(slicepairs[spi]), horizontalalignment='left', verticalalignment='bottom')
         pp.savefig()
+    annotate_pdf_metadata(pp, scriptname="finiterectlat-constant-driving.py")
     pp.close()
 
 exit(0)

misc/finiterectlat-modes.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 import math
-from qpms.argproc import ArgParser
+from qpms.argproc import ArgParser, annotate_pdf_metadata
 
 
 ap = ArgParser(['rectlattice2d_finite', 'background_analytical', 'single_particle', 'single_lMax', ])
@@ -100,7 +100,7 @@ results['inside_contour'] = inside_ellipse((results['eigval'].real, results['eig
 results['refractive_index_internal'] = [medium(om).n for om in results['eigval']]
 
 outfile = defaultprefix + (('_ir%s_%s.npz' % (str(iri), irname)) if iri is not None else '.npz') if a.output is None else a.output
-np.savez(outfile, meta=vars(a), **results)
+np.savez(outfile, meta={**vars(a), 'qpms_version' : qpms.__version__()}, **results)
 logging.info("Saved to %s" % outfile)
 
 exit(0)
@@ -110,7 +110,7 @@ if a.plot or (a.plot_out is not None):
     import matplotlib
     matplotlib.use('pdf')
     from matplotlib import pyplot as plt
-
+    from matplotlib.backends.backend_pdf import PdfPages
     fig = plt.figure()
     ax = fig.add_subplot(111)
     ax.plot(sinalpha_list, σ_ext*1e12,label='$\sigma_\mathrm{ext}$')
@@ -119,9 +119,11 @@ if a.plot or (a.plot_out is not None):
     ax.legend()
     ax.set_xlabel('$\sin\\alpha$')
     ax.set_ylabel('$\sigma/\mathrm{\mu m^2}$')
-    
+        
     plotfile = defaultprefix + ".pdf" if a.plot_out is None else a.plot_out
-    fig.savefig(plotfile)
+    with PdfPages(plotfile) as pdf:
+        pdf.savefig(fig)
+        annotate_pdf_metadata(pdf, scriptname='finiterectlat-modes.py')
 
 exit(0)
 

misc/finiterectlat-scatter.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 
+from qpms.argproc import ArgParser, annotate_pdf_metadata
 import math
 pi = math.pi
-from qpms.argproc import ArgParser
 
 
 ap = ArgParser(['rectlattice2d_finite', 'single_particle', 'single_lMax', 'omega_seq_real_ng', 'planewave'])
@@ -111,7 +111,7 @@ for i, omega in enumerate(ap.allomegas):
             σ_scat_arr_ir[i, j, iri] = np.vdot(fi,np.dot(translation_matrix, fi)).real/wavenumber**2
         if a.save_gradually:
             iriout = outfile_tmp + ".%d.%d" % (i, iri)
-            np.savez(iriout, omegai=i, iri=iri, meta=vars(a), omega=omega, k_sph=k_sph_list, k_cart = k_cart_arr, E_cart=E_cart_list, E_sph=np.array(E_sph),
+            np.savez(iriout, omegai=i, iri=iri, meta={**vars(a), 'qpms_version' : qpms.__version__()}, omega=omega, k_sph=k_sph_list, k_cart = k_cart_arr, E_cart=E_cart_list, E_sph=np.array(E_sph),
                      wavenumber=wavenumber, σ_ext_list_ir=σ_ext_arr_ir[i,:,iri], σ_scat_list_ir=σ_scat_list_ir[i,:,iri])
             logging.info("partial results saved to %s"%iriout)
 
@@ -122,7 +122,8 @@ for i, omega in enumerate(ap.allomegas):
 
 
 outfile = defaultprefix + ".npz" if a.output is None else a.output
-np.savez(outfile, meta=vars(a), k_sph=k_sph_list, k_cart = k_cart_arr, E_cart=E_cart_list, E_sph=np.array(E_sph),
+np.savez(outfile, meta={**vars(a), 'qpms_version' : qpms.__version__()}, 
+        k_sph=k_sph_list, k_cart = k_cart_arr, E_cart=E_cart_list, E_sph=np.array(E_sph),
         σ_ext=σ_ext_arr,σ_abs=σ_abs_arr,σ_scat=σ_scat_arr,
         σ_ext_ir=σ_ext_arr_ir,σ_abs_ir=σ_abs_arr_ir,σ_scat_ir=σ_scat_arr_ir, omega=ap.allomegas, wavenumbers=wavenumbers
        )
@@ -231,6 +232,7 @@ if a.plot or (a.plot_out is not None):
 
             pdf.savefig(fig)
             plt.close(fig)
+        annotate_pdf_metadata(pdf, scriptname="finiterectlat-scatter.py")
 
 
 exit(0)

misc/infiniterectlat-k0realfreqsvd.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 import math
-from qpms.argproc import ArgParser
+from qpms.argproc import ArgParser, annotate_pdf_metadata
 
 ap = ArgParser(['rectlattice2d', 'single_particle', 'single_lMax', 'omega_seq'])
 ap.add_argument("-o", "--output", type=str, required=False, help='output path (if not provided, will be generated automatically)')
@@ -93,7 +93,7 @@ for i, omega in enumerate(omegas):
         SVs[iri][i] = np.linalg.svd(ImTW_packed, compute_uv = False)
 
 outfile = defaultprefix + ".npz" if a.output is None else a.output
-np.savez(outfile, meta=vars(a), omegas=omegas, wavenumbers=wavenumbers, SVs=np.concatenate(SVs, axis=-1), irrep_names=ss1.irrep_names, irrep_sizes=ss1.saecv_sizes, unitcell_area=ss.unitcell_volume
+np.savez(outfile, meta={**vars(a), 'qpms_version' : qpms.__version__()}, omegas=omegas, wavenumbers=wavenumbers, SVs=np.concatenate(SVs, axis=-1), irrep_names=ss1.irrep_names, irrep_sizes=ss1.saecv_sizes, unitcell_area=ss.unitcell_volume
        )
 logging.info("Saved to %s" % outfile)
 
@@ -102,7 +102,8 @@ if a.plot or (a.plot_out is not None):
     import matplotlib
     matplotlib.use('pdf')
     from matplotlib import pyplot as plt
-
+    from matplotlib.backends.backend_pdf import PdfPages
+    
     fig = plt.figure()
     ax = fig.add_subplot(111)
     cc = plt.rcParams['axes.prop_cycle']()
@@ -117,9 +118,11 @@ if a.plot or (a.plot_out is not None):
     ax.set_xlabel('$\hbar \omega / \mathrm{eV}$')
     ax.set_ylabel('Singular values')
     ax.legend()
-    
+
     plotfile = defaultprefix + ".pdf" if a.plot_out is None else a.plot_out
-    fig.savefig(plotfile)
+    with PdfPages(plotfile) as pdf:
+        pdf.savefig(fig)
+        annotate_pdf_metadata(pdf, scriptname='infiniterectlat-k0realfreqsvd.py')
 
 exit(0)
 

misc/infiniterectlat-scatter.py

@@ -2,7 +2,7 @@
 
 import math
 pi = math.pi
-from qpms.argproc import ArgParser
+from qpms.argproc import ArgParser, annotate_pdf_metadata
 
 ap = ArgParser(['rectlattice2d', 'single_particle', 'single_lMax', 'omega_seq_real_ng', 'planewave'])
 ap.add_argument("-o", "--output", type=str, required=False, help='output path (if not provided, will be generated automatically)')
@@ -106,7 +106,7 @@ with pgsl_ignore_error(15): # avoid gsl crashing on underflow
 σ_abs_arr = σ_ext_arr - σ_scat_arr
 
 outfile = defaultprefix + ".npz" if a.output is None else a.output
-np.savez(outfile, meta=vars(a), dir_sph=dir_sph_list, k_cart = k_cart_arr, omega = ap.allomegas, E_cart = E_cart_list, wavenumbers= wavenumbers, σ_ext=σ_ext_arr,σ_abs=σ_abs_arr,σ_scat=σ_scat_arr, unitcell_area=ss.unitcell_volume
+np.savez(outfile, meta={**vars(a), 'qpms_version' : qpms.__version__()}, dir_sph=dir_sph_list, k_cart = k_cart_arr, omega = ap.allomegas, E_cart = E_cart_list, wavenumbers= wavenumbers, σ_ext=σ_ext_arr,σ_abs=σ_abs_arr,σ_scat=σ_scat_arr, unitcell_area=ss.unitcell_volume
        )
 logging.info("Saved to %s" % outfile)
 
@@ -214,6 +214,6 @@ if a.plot or (a.plot_out is not None):
             
             pdf.savefig(fig)
             plt.close(fig)
-
+        annotate_pdf_metadata(pdf)
 exit(0)
 

misc/lat2d_modes.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 import math
-from qpms.argproc import ArgParser, sfloat
+from qpms.argproc import ArgParser, sfloat, annotate_pdf_metadata
 
 ap = ArgParser(['const_real_background', 'lattice2d', 'multi_particle']) # TODO general analytical background
     
@@ -112,7 +112,7 @@ res['inside_contour'] = inside_ellipse((res['eigval'].real, res['eigval'].imag),
 #del res['omega']  If contour points are not needed...
 #del res['ImTW'] # not if dbg=false anyway
 outfile = defaultprefix + ".npz" if a.output is None else a.output
-np.savez(outfile, meta=vars(a), empty_freqs=np.array(empty_freqs), 
+np.savez(outfile, meta={**vars(a), 'qpms_version' : qpms.__version__()}, empty_freqs=np.array(empty_freqs), 
         ss_positions=ss.positions, ss_fullvec_poffsets=ss.fullvec_poffsets, 
         ss_fullvec_psizes=ss.fullvec_psizes,
         ss_bspecs_flat = np.concatenate(ss.bspecs),
@@ -132,6 +132,7 @@ if a.plot or (a.plot_out is not None):
     import matplotlib
     matplotlib.use('pdf')
     from matplotlib import pyplot as plt
+    from matplotlib.backends.backend_pdf import PdfPages
 
     fig = plt.figure()
     ax = fig.add_subplot(111,)
@@ -155,8 +156,11 @@ if a.plot or (a.plot_out is not None):
     ax.set_ylim([ymin-.1*yspan, ymax+.1*yspan])
     ax.set_xlabel('$\hbar \Re \omega / \mathrm{eV}$')
     ax.set_ylabel('$\hbar \Im \omega / \mathrm{meV}$')
+
     plotfile = defaultprefix + ".pdf" if a.plot_out is None else a.plot_out
-    fig.savefig(plotfile)
+    with PdfPages(plotfile) as pdf:
+        pdf.savefig(fig)
+        annotate_pdf_metadata(pdf, scriptname='lat2d_modes.py')
 
 exit(0)
 

misc/lat2d_realfreqsvd.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 import math
-from qpms.argproc import ArgParser, sfloat
+from qpms.argproc import ArgParser, sfloat, annotate_pdf_metadata
 
 ap = ArgParser(['background', 'lattice2d', 'multi_particle',  'omega_seq'])
 
@@ -88,7 +88,7 @@ for i, omega in enumerate(omegas):
         SVs[iri][i] = np.linalg.svd(ImTW_packed, compute_uv = False)
 
 outfile = defaultprefix + ".npz" if a.output is None else a.output
-np.savez(outfile, meta=vars(a), omegas=omegas, wavenumbers=wavenumbers, SVs=np.concatenate(SVs, axis=-1), irrep_names=ss1.irrep_names, irrep_sizes=ss1.saecv_sizes, unitcell_area=ss.unitcell_volume
+np.savez(outfile, meta={**vars(a), 'qpms_version' : qpms.__version__()}, omegas=omegas, wavenumbers=wavenumbers, SVs=np.concatenate(SVs, axis=-1), irrep_names=ss1.irrep_names, irrep_sizes=ss1.saecv_sizes, unitcell_area=ss.unitcell_volume
        )
 logging.info("Saved to %s" % outfile)
 
@@ -97,6 +97,7 @@ if a.plot or (a.plot_out is not None):
     import matplotlib
     matplotlib.use('pdf')
     from matplotlib import pyplot as plt
+    from matplotlib.backends.backend_pdf import PdfPages
 
     fig = plt.figure()
     ax = fig.add_subplot(111)
@@ -118,9 +119,11 @@ if a.plot or (a.plot_out is not None):
     ax.set_xlabel('$\hbar \omega / \mathrm{eV}$')
     ax.set_ylabel('Singular values')
     ax.legend()
-    
+
     plotfile = defaultprefix + ".pdf" if a.plot_out is None else a.plot_out
-    fig.savefig(plotfile)
+    with PdfPages(plotfile) as pdf:
+        pdf.savefig(fig)
+        annotate_pdf_metadata(pdf, scriptname='lat2d_realfreqsvd.py')
 
 exit(0)
 

misc/rectlat_simple_modes.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 import math
-from qpms.argproc import ArgParser
+from qpms.argproc import ArgParser, annotate_pdf_metadata
 
 ap = ArgParser(['rectlattice2d', 'const_real_background', 'single_particle', 'single_lMax']) # const_real_background needed for calculation of the diffracted orders
 ap.add_argument("-k", nargs=2, type=float, required=True, help='k vector', metavar=('K_X', 'K_Y'))
@@ -116,7 +116,7 @@ res['refractive_index_internal'] = [emg(om).n for om in res['eigval']]
 #del res['omega']  If contour points are not needed...
 #del res['ImTW'] # not if dbg=false anyway
 outfile = defaultprefix + ".npz" if a.output is None else a.output
-np.savez(outfile, meta=vars(a), empty_freqs=np.array(empty_freqs), 
+np.savez(outfile, meta={**vars(a), 'qpms_version' : qpms.__version__()}, empty_freqs=np.array(empty_freqs), 
         ss_positions=ss.positions, ss_fullvec_poffsets=ss.fullvec_poffsets, 
         ss_fullvec_psizes=ss.fullvec_psizes,
         ss_bspecs_flat = np.concatenate(ss.bspecs),
@@ -133,6 +133,7 @@ if a.plot or (a.plot_out is not None):
     import matplotlib
     matplotlib.use('pdf')
     from matplotlib import pyplot as plt
+    from matplotlib.backends.backend_pdf import PdfPages
 
     fig = plt.figure()
     ax = fig.add_subplot(111,)
@@ -156,8 +157,11 @@ if a.plot or (a.plot_out is not None):
     ax.set_ylim([ymin-.1*yspan, ymax+.1*yspan])
     ax.set_xlabel('$\hbar \Re \omega / \mathrm{eV}$')
     ax.set_ylabel('$\hbar \Im \omega / \mathrm{meV}$')
+
     plotfile = defaultprefix + ".pdf" if a.plot_out is None else a.plot_out
-    fig.savefig(plotfile)
+    with PdfPages(plotfile) as pdf:
+        pdf.savefig(fig)
+        annotate_pdf_metadata(pdf, scriptname="rectlat_simple_modes.py")
 
 exit(0)
 

notes/INSTALL_ANDROID.md

@@ -0,0 +1,107 @@
+# Installing QPMS on Android/AOSP (-based) systems
+
+Yes, it is possible. Basically all you need is a device capable of running [Termux](https://termux.com/) with enough memory to build everything.
+
+The following instructions have been tested with Termux version 0.118.0 on
+[e/OS/ R development build on a Samsung Galaxy S10e](https://doc.e.foundation/devices/beyond0lte/install)
+([e-1.0-r-20220526188878-dev-beyond0lte](https://images.ecloud.global/dev/beyond0lte/)).
+Presumably, they should work also on stock Android as well, but who
+in their right mind would run all the spyware by Google & al.?
+
+Physical keyboard or [remote access](https://wiki.termux.com/wiki/Remote_Access) is strongly recommended. :D
+
+## Get Termux
+
+Just [install the Termux app from F-Droid or Github as per instructions](https://github.com/termux/termux-app#f-droid).
+
+Open Termux; the following steps of these instructions are basically
+just commands you need to type in Termux.
+
+## Install prerequisities from termux repositories
+
+```
+pkg install python3 cmake git clang build-essential binutils
+```
+
+## Build and install GSL
+
+```
+curl -O https://www.nic.funet.fi/pub/gnu/ftp.gnu.org/pub/gnu/gsl/gsl-latest.tar.gz
+tar xf gsl-latest.tar.gz
+cd gsl-2.7.1
+./configure --prefix=$PREFIX
+make    # add -j4 or so to make it faster on multicore systems
+make install
+cd -
+```
+
+## Build and install OpenBLAS
+
+```
+git clone https://github.com/xianyi/OpenBLAS.git
+cd OpenBLAS
+make
+make PREFIX=$PREFIX install
+cd -
+```
+
+### Workaround for "broken" setup.py script
+
+The goal is to fix `setup.py` so that it finds the correct libraries automatically, but in the meantime, you can use this workaround to get the Python part of QPMS installed:
+
+```
+ln -s $PREFIX/lib/libopenblas.so $PREFIX/LIB/liblapacke.so
+```
+
+## Build and install Numpy
+
+(Successful build requires the `MATHLIB` environmental variable set, otherwise linking will fail; see https://wiki.termux.com/wiki/Python.)
+
+```
+MATHLIB=m pip3 install numpy
+```
+
+### Install Sympy
+
+```
+pip3 install sympy
+```
+
+## Build and install QPMS
+
+```
+git clone https://repo.or.cz/qpms.git
+cd qpms
+cmake -DCMAKE_INSTALL_PREFIX=$PREFIX . # ugly, TODO make a separate build tree!
+make install
+
+python3 setup.py install
+```
+
+Hopefully, QPMS has installed successfully. At this point, you should be able
+to import and use QPMS with some exceptions. First, there is some legacy code
+in the `qpms.qpms_p` module (which is no longer imported automatically with
+bare `import qpms`). You shouldn't need this unless you are trying to run some
+historic Jupyter notebooks or other old custom scripts. It contains a scipy
+dependence, and scipy is hard to get working in Android environment (as
+it requires a Fortran compiler to build).
+
+## Install matplotlib
+
+If you try to run just `pip3 install matplotlib` in Termux, it might likely
+fail when installing the `pillow` dependency.
+First, according to [Termux wiki](https://wiki.termux.com/wiki/Python#Python_module_installation_tips_and_tricks),
+pillow depends on `libpng` and `libjpeg-turbo`, which are fortunately
+available in Termux packages.
+Second, pillow instalation requires an additional environment variable
+`LDFLAGS="-L/system/lib64"` to be set on 64-bit devices.
+
+Hence:
+```
+pkg install libpng libjpeg-turbo
+export LDFLAGS="-L/system/lib64" # on 64-bit devices
+pip3 install matplotlib
+```
+
+After this step, you should be able to run the command-line scripts
+from `misc/` directory and examples from `examples/` directory.

qpms/CMakeLists.txt

@@ -7,15 +7,23 @@ find_package(LAPACK REQUIRED)
 # and other not very relevant warnings
 set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-int-in-bool-context -Wno-comment")
 
+# version file
+include(GetGitRevisionDescription)
+get_git_head_revision(GIT_REFSPEC GIT_SHA1)
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/version.c.in" "${CMAKE_CURRENT_BINARY_DIR}/version.c" @ONLY)
+list(APPEND SOURCES "${CMAKE_CURRENT_BINARY_DIR}/version.c" version.h)
+
 #includes
 set (DIRS ${GSL_INCLUDE_DIRS} ${GSLCBLAS_INCLUDE_DIRS})
 include_directories(${DIRS})
 
+
+
 add_library (qpms SHARED translations.c tmatrices.c vecprint.c vswf.c wigner.c ewald.c
 	ewaldsf.c pointgroups.c latticegens.c
 	lattices2d.c gaunt.c error.c legendre.c symmetries.c vecprint.c
 	bessel.c own_zgemm.c parsing.c scatsystem.c materials.c drudeparam_data.c
-	lll.c beyn.c trivialgroup.c
+	lll.c beyn.c trivialgroup.c version.c
 	)
 use_c99()
 
@@ -23,9 +31,9 @@ set(LIBS ${LIBS} ${GSL_LIBRARIES} ${GSLCBLAS_LIBRARIES})
 
 
 target_link_libraries (qpms
-	gsl
-	lapack
-	blas
+	${GSL_LIBRARIES}
+	${LAPACK_LIBRARIES}
+	${BLAS_LIBRARIES}
 	${QPMS_AMOSLIB}
 	Faddeeva
 	)

qpms/__init__.py

@@ -1,5 +1,3 @@
-from pkg_resources import get_distribution
-__version__ = get_distribution('qpms').version
 
 import os as __os
 from sys import platform as __platform
@@ -7,7 +5,7 @@ from sys import platform as __platform
 import warnings as __warnings
 
 try:
-    from .qpms_c import PointGroup, FinitePointGroup, FinitePointGroupElement, Particle, scatsystem_set_nthreads, ScatteringSystem, ScatteringMatrix, pitau, set_gsl_pythonic_error_handling, pgsl_ignore_error, gamma_inc, lll_reduce
+    from .qpms_c import PointGroup, FinitePointGroup, FinitePointGroupElement, Particle, scatsystem_set_nthreads, ScatteringSystem, ScatteringMatrix, pitau, set_gsl_pythonic_error_handling, pgsl_ignore_error, gamma_inc, lll_reduce, qpms_library_version
 except ImportError as ex:
     if __platform == "linux" or __platform == "linux2":
         if 'LD_LIBRARY_PATH' not in __os.environ.keys():
@@ -24,7 +22,12 @@ from .cymaterials import MaterialInterpolator, EpsMu, LorentzDrudeModel, lorentz
 from .cycommon import dbgmsg_enable, dbgmsg_disable, dbgmsg_active, BesselType, VSWFType
 from .cywaves import vswf_single
 
-from .qpms_p import * # maybe don't import automatically in the future (adds around 0.5 s delay)
+def __version__():
+    from pkg_resources import get_distribution
+    librev = qpms_library_version()
+    return get_distribution('qpms').version + (("lr:"+librev) if librev else "")
+
+#from .qpms_p import * # don't import automatically (adds around 0.5 s delay and depends on scipy)
 from .constants import *
 
 # legacy code which brutally slows down the whole package init:

qpms/argproc.py

@@ -540,3 +540,22 @@ class ArgParser:
             plist.extend([Particle(pos, t, bspec=bspec) for pos in poss])
         return plist
 
+#TODO perhaps move into another module
+def annotate_pdf_metadata(pdfPages, scriptname=None, keywords=None, author=None, title=None, subject=None, **kwargs):
+    """Adds QPMS version-related metadata to a matplotlib PdfPages object
+
+    Use before closing the PDF file.
+    """
+    from .qpms_c import qpms_library_version
+    d = pdfPages.infodict()
+    d['Creator'] = "QPMS%s (lib rev. %s), https://qpms.necada.org" % (
+        "" if scriptname is None else (" "+scriptname), qpms_library_version())
+    if author is not None:
+        d['Author'] = author
+    if title is not None:
+        d['Title'] = title
+    if subject is not None:
+        d['Subject'] = subject
+    if keywords is not None:
+        d['Keywords'] = ' '.join(keywords)
+    d.update(kwargs) 

qpms/constants.py

@@ -1,7 +1,26 @@
-# unit conversions, mostly for standalone usage
-# TODO avoid importing the "heavy" qpms parts
-from scipy.constants import epsilon_0 as ε_0, c, pi as π, e as eV, hbar, hbar as ℏ, mu_0 as μ_0
-pi = π
+"""
+Constants and unit conversion, mostly for standalode usage.
+
+Previously, QPMS used scipy.constants in the python parts.
+Now the relevant ones are set explicitly here in order
+to avoid dependency on the whole scipy (which needs a fortran
+compiler to build.
+
+The values are taken from scipy / "2018 CODATA recommended values".
+They slightly differ from the constants in GSL that are used
+in the C code. It would be desirable to use the same source,
+hence the values here might be subject to change in future versions.
+"""
+
+epsilon_0 = ε_0 = 8.8541878128e-12  # ± 0.0000000013e-12      F m^-1
+c = speed_of_light = 299792458.
+eV = e = elementary_charge = 1.602176487e-19  # ± 0000000040e-19    C
+hbar = ℏ = 1.054571800e-34  #  ± 0.000000013e-34    J s
+mu_0 = μ_0 = 1.25663706212e-6  #  ± 0.00000000019 e-6     N A^-2
+
+from math import pi
+π = pi
+
 μm = 1e-6
 nm = 1e-9
 # "SCUFF FREQUENCY UNIT"

qpms/cymaterials.pxd

@@ -18,7 +18,7 @@ cdef class MaterialInterpolator:
     cdef readonly double omegamin
     cdef readonly double omegamax
     cdef inline void *rawpointer(self):
-        return <void *>&(self.interp)
+        return <void *>(self.interp)
 
 cdef class EpsMu:
     cdef public qpms_epsmu_t em

qpms/cymaterials.pyx

@@ -9,7 +9,7 @@ cimport cython
 import enum
 import warnings
 import os
-from scipy.constants import e as eV, hbar, c
+from .constants import e as eV, hbar, c
 from libc.stdlib cimport malloc, free, calloc, abort
 
 class EpsMuGeneratorType(enum.Enum):

qpms/qpms_c.pyx

@@ -17,6 +17,9 @@ from .cymaterials cimport EpsMuGenerator, EpsMu
 from libc.stdlib cimport malloc, free, calloc
 import warnings
 
+def qpms_library_version():
+    return "git_" + qpms_version_git_sha1.decode('utf-8')
+
 from cython.parallel cimport prange, parallel
 from cython cimport boundscheck, wraparound
 

qpms/qpms_cdefs.pxd

@@ -4,6 +4,9 @@ ctypedef double complex cdouble
 
 from libc.stdint cimport *
 
+cdef extern from "version.h":
+    const char *qpms_version_git_sha1
+
 cdef extern from "gsl/gsl_errno.h":
     ctypedef void gsl_error_handler_t (const char *reason, const char *file,
             int line, int gsl_errno)

qpms/qpms_p.py

@@ -6,7 +6,7 @@ import numpy as np
 from .qpms_c import *
 ň = np.newaxis
 import scipy
-from scipy.constants import epsilon_0 as ε_0, c, pi as π, e, hbar as ℏ, mu_0 as μ_0
+from .constants import ε_0, c, pi, π, e, ℏ, μ_0
 eV = e
 from scipy.special import lpmn, lpmv, spherical_jn, spherical_yn, poch, gammaln, factorial
 import math

qpms/scatsystem.c

@@ -1295,7 +1295,6 @@ static inline complex double *qpms_scatsysw_scatsyswk_build_modeproblem_matrix_f
     QPMS_CRASHING_MALLOC(target, SQ(full_len) * sizeof(complex double));
   complex double *tmp; // translation matrix, S or W
   QPMS_CRASHING_MALLOC(tmp, SQ(ss->max_bspecn) * sizeof(complex double));
-  memset(target, 0, SQ(full_len) * sizeof(complex double));
   const complex double zero = 0, minusone = -1;
   { // Non-diagonal part; M[piR, piC] = -T[piR] S(piR<-piC)
     size_t fullvec_offsetR = 0;
@@ -1321,7 +1320,14 @@ static inline complex double *qpms_scatsysw_scatsyswk_build_modeproblem_matrix_f
                 QPMS_EWALD_FULL, eta));
         }
 
-        cblas_zgemm(CblasRowMajor, CblasNoTrans, CblasNoTrans,
+        if (k == NULL && piC == piR) { 
+          // non-periodic case diagonal block: no "self-interaction", just
+          // fill with zeroes (the ones on the diagonal are added in the very end)
+          QPMS_ENSURE_SUCCESS(LAPACKE_zlaset(CblasRowMajor, 'x',
+                bspecR->n /*m*/, bspecC->n/*n*/, 0 /*alfa: offdiag*/, 0 /*beta: diag*/, 
+                target + fullvec_offsetR*full_len + fullvec_offsetC /*a*/,
+                full_len /*lda*/));
+        } else cblas_zgemm(CblasRowMajor, CblasNoTrans, CblasNoTrans,
             bspecR->n /*m*/, bspecC->n /*n*/, bspecR->n /*k*/, 
             &minusone/*alpha*/, tmmR/*a*/, bspecR->n/*lda*/,
             tmp/*b*/, bspecC->n/*ldb*/, &zero/*beta*/,

qpms/symmetries.py

@@ -1,5 +1,6 @@
+import sympy
 from sympy.combinatorics import Permutation, PermutationGroup
-Permutation.print_cyclic = True
+sympy.init_printing(perm_cyclic = True)
 import cmath
 from cmath import exp, pi
 from math import sqrt

qpms/tmatrices.py

@@ -12,8 +12,7 @@ except ImportError:
     use_moble_quaternion = False
 
 import re
-from scipy import interpolate
-from scipy.constants import hbar, e as eV, pi, c
+from .constants import hbar, eV, pi, c
 from .cycommon import get_mn_y, get_nelem
 from .cyquaternions import CQuat
 ň = np.newaxis
@@ -440,6 +439,7 @@ class TMatrix(TMatrixSpec):
     TODO support for different/multiple interpolators
     '''
     def __init__(self, tmatrix_spec):
+        from scipy import interpolate
         #self.specification = tmatrix_spec
         self.lMax_override = tmatrix_spec.lMax_override
         self.tmatrix_path = tmatrix_spec.tmatrix_path

qpms/version.c.in

@@ -0,0 +1,2 @@
+#define QPMS_GIT_SHA1 "@GIT_SHA1@"
+const char qpms_version_git_sha1[] = QPMS_GIT_SHA1;

qpms/version.h

@@ -0,0 +1,4 @@
+#ifndef QPMS_VERSION_H
+#define QPMS_VERSION_H
+extern const char qpms_version_git_sha1[];
+#endif //QPMS_VERSION_H

qpms/vswf.c

@@ -131,7 +131,7 @@ size_t *qpms_vswf_set_reindex(const qpms_vswf_set_spec_t *small, const qpms_vswf
     while(big_pairs[bi].ui < small_pairs[si].ui) 
       ++bi;
     if(big_pairs[bi].ui == small_pairs[si].ui)
-      r[small_pairs[si].i_orig] = big_pairs[si].i_orig;
+      r[small_pairs[si].i_orig] = big_pairs[bi].i_orig;
     else
       r[small_pairs[si].i_orig] = ~(size_t)0;
   }

setup.py

@@ -161,7 +161,7 @@ setup(name='qpms',
         setup_requires=['cython>=0.28','numpy>=1.2','setuptools>=18.0'],
         install_requires=['cython>=0.28',
             #'quaternion','spherical_functions',
-            'scipy>=0.18.0', 'sympy>=1.2', 'numpy>=1.2'],
+            'sympy>=1.2', 'numpy>=1.2'],
         #dependency_links=['https://github.com/moble/quaternion/archive/v2.0.tar.gz','https://github.com/moble/spherical_functions/archive/master.zip'],
         ext_modules=cythonize([qpms_c, cywaves, cytranslations, cytmatrices, cycommon, cyquaternions, cybspec, cymaterials, cyewaldtest], include_path=['qpms', 'amos'], gdb_debug=True),
         cmdclass = {'build_ext': build_ext},