Merge branch 'master' of bitbucket.org:glavaux/cosmotool

.gitignore

@@ -1,4 +1,9 @@
 *~
+.eggs/
+dist/
+wheelhouse/
+cosmotool.egg-info/
+build/
 *.o
 *.prog
 *.pyc

CMakeLists.txt

@@ -54,8 +54,8 @@ IF(YORICK_SUPPORT)
   ENDIF((EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4") OR (INTERNAL_NETCDF))
 ENDIF(YORICK_SUPPORT)
 
-find_program(CYTHON cython3 cython)
+find_program(CYTHON NAMES cython3 cython)
-find_library(ZLIB z)
+find_library(ZLIB_LIBRARY z)
 find_library(DL_LIBRARY dl)
 find_library(MATH_LIBRARY m)
 
@@ -70,8 +70,8 @@ SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "A toolbox for impatient cosmologists")
 SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
-SET(CPACK_PACKAGE_VERSION_MINOR "0")
+SET(CPACK_PACKAGE_VERSION_MINOR "1")
-SET(CPACK_PACKAGE_VERSION_PATCH "0${EXTRA_VERSION}")
+SET(CPACK_PACKAGE_VERSION_PATCH "1${EXTRA_VERSION}")
 SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")
 SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
 SET(CPACK_SOURCE_IGNORE_FILES 

LICENCE.txt

@@ -0,0 +1,508 @@
+Copyright (C) 2009-2020 Guilhem Lavaux
+
+
+CeCILL FREE SOFTWARE LICENSE AGREEMENT
+
+
+    Notice
+
+This Agreement is a Free Software license agreement that is the result
+of discussions between its authors in order to ensure compliance with
+the two main principles guiding its drafting:
+
+    * firstly, compliance with the principles governing the distribution
+      of Free Software: access to source code, broad rights granted to
+      users,
+    * secondly, the election of a governing law, French law, with which
+      it is conformant, both as regards the law of torts and
+      intellectual property law, and the protection that it offers to
+      both authors and holders of the economic rights over software.
+
+The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+license are:
+
+Commissariat à l'Energie Atomique - CEA, a public scientific, technical
+and industrial research establishment, having its principal place of
+business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+
+Centre National de la Recherche Scientifique - CNRS, a public scientific
+and technological establishment, having its principal place of business
+at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+
+Institut National de Recherche en Informatique et en Automatique -
+INRIA, a public scientific and technological establishment, having its
+principal place of business at Domaine de Voluceau, Rocquencourt, BP
+105, 78153 Le Chesnay cedex, France.
+
+
+    Preamble
+
+The purpose of this Free Software license agreement is to grant users
+the right to modify and redistribute the software governed by this
+license within the framework of an open source distribution model.
+
+The exercising of these rights is conditional upon certain obligations
+for users so as to preserve this status for all subsequent redistributions.
+
+In consideration of access to the source code and the rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors only have limited liability.
+
+In this respect, the risks associated with loading, using, modifying
+and/or developing or reproducing the software by the user are brought to
+the user's attention, given its Free Software status, which may make it
+complicated to use, with the result that its use is reserved for
+developers and experienced professionals having in-depth computer
+knowledge. Users are therefore encouraged to load and test the
+suitability of the software as regards their requirements in conditions
+enabling the security of their systems and/or data to be ensured and,
+more generally, to use and operate it in the same conditions of
+security. This Agreement may be freely reproduced and published,
+provided it is not altered, and that no provisions are either added or
+removed herefrom.
+
+This Agreement may apply to any or all software for which the holder of
+the economic rights decides to submit the use thereof to its provisions.
+
+
+    Article 1 - DEFINITIONS
+
+For the purpose of this Agreement, when the following expressions
+commence with a capital letter, they shall have the following meaning:
+
+Agreement: means this license agreement, and its possible subsequent
+versions and annexes.
+
+Software: means the software in its Object Code and/or Source Code form
+and, where applicable, its documentation, "as is" when the Licensee
+accepts the Agreement.
+
+Initial Software: means the Software in its Source Code and possibly its
+Object Code form and, where applicable, its documentation, "as is" when
+it is first distributed under the terms and conditions of the Agreement.
+
+Modified Software: means the Software modified by at least one
+Contribution.
+
+Source Code: means all the Software's instructions and program lines to
+which access is required so as to modify the Software.
+
+Object Code: means the binary files originating from the compilation of
+the Source Code.
+
+Holder: means the holder(s) of the economic rights over the Initial
+Software.
+
+Licensee: means the Software user(s) having accepted the Agreement.
+
+Contributor: means a Licensee having made at least one Contribution.
+
+Licensor: means the Holder, or any other individual or legal entity, who
+distributes the Software under the Agreement.
+
+Contribution: means any or all modifications, corrections, translations,
+adaptations and/or new functions integrated into the Software by any or
+all Contributors, as well as any or all Internal Modules.
+
+Module: means a set of sources files including their documentation that
+enables supplementary functions or services in addition to those offered
+by the Software.
+
+External Module: means any or all Modules, not derived from the
+Software, so that this Module and the Software run in separate address
+spaces, with one calling the other when they are run.
+
+Internal Module: means any or all Module, connected to the Software so
+that they both execute in the same address space.
+
+GNU GPL: means the GNU General Public License version 2 or any
+subsequent version, as published by the Free Software Foundation Inc.
+
+Parties: mean both the Licensee and the Licensor.
+
+These expressions may be used both in singular and plural form.
+
+
+    Article 2 - PURPOSE
+
+The purpose of the Agreement is the grant by the Licensor to the
+Licensee of a non-exclusive, transferable and worldwide license for the
+Software as set forth in Article 5 hereinafter for the whole term of the
+protection granted by the rights over said Software. 
+
+
+    Article 3 - ACCEPTANCE
+
+3.1 The Licensee shall be deemed as having accepted the terms and
+conditions of this Agreement upon the occurrence of the first of the
+following events:
+
+    * (i) loading the Software by any or all means, notably, by
+      downloading from a remote server, or by loading from a physical
+      medium;
+    * (ii) the first time the Licensee exercises any of the rights
+      granted hereunder.
+
+3.2 One copy of the Agreement, containing a notice relating to the
+characteristics of the Software, to the limited warranty, and to the
+fact that its use is restricted to experienced users has been provided
+to the Licensee prior to its acceptance as set forth in Article 3.1
+hereinabove, and the Licensee hereby acknowledges that it has read and
+understood it.
+
+
+    Article 4 - EFFECTIVE DATE AND TERM
+
+
+      4.1 EFFECTIVE DATE
+
+The Agreement shall become effective on the date when it is accepted by
+the Licensee as set forth in Article 3.1.
+
+
+      4.2 TERM
+
+The Agreement shall remain in force for the entire legal term of
+protection of the economic rights over the Software.
+
+
+    Article 5 - SCOPE OF RIGHTS GRANTED
+
+The Licensor hereby grants to the Licensee, who accepts, the following
+rights over the Software for any or all use, and for the term of the
+Agreement, on the basis of the terms and conditions set forth hereinafter.
+
+Besides, if the Licensor owns or comes to own one or more patents
+protecting all or part of the functions of the Software or of its
+components, the Licensor undertakes not to enforce the rights granted by
+these patents against successive Licensees using, exploiting or
+modifying the Software. If these patents are transferred, the Licensor
+undertakes to have the transferees subscribe to the obligations set
+forth in this paragraph.
+
+
+      5.1 RIGHT OF USE
+
+The Licensee is authorized to use the Software, without any limitation
+as to its fields of application, with it being hereinafter specified
+that this comprises:
+
+   1. permanent or temporary reproduction of all or part of the Software
+      by any or all means and in any or all form.
+
+   2. loading, displaying, running, or storing the Software on any or
+      all medium.
+
+   3. entitlement to observe, study or test its operation so as to
+      determine the ideas and principles behind any or all constituent
+      elements of said Software. This shall apply when the Licensee
+      carries out any or all loading, displaying, running, transmission
+      or storage operation as regards the Software, that it is entitled
+      to carry out hereunder.
+
+
+      5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+
+The right to make Contributions includes the right to translate, adapt,
+arrange, or make any or all modifications to the Software, and the right
+to reproduce the resulting software.
+
+The Licensee is authorized to make any or all Contributions to the
+Software provided that it includes an explicit notice that it is the
+author of said Contribution and indicates the date of the creation thereof.
+
+
+      5.3 RIGHT OF DISTRIBUTION
+
+In particular, the right of distribution includes the right to publish,
+transmit and communicate the Software to the general public on any or
+all medium, and by any or all means, and the right to market, either in
+consideration of a fee, or free of charge, one or more copies of the
+Software by any means.
+
+The Licensee is further authorized to distribute copies of the modified
+or unmodified Software to third parties according to the terms and
+conditions set forth hereinafter.
+
+
+        5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+
+The Licensee is authorized to distribute true copies of the Software in
+Source Code or Object Code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+   1. a copy of the Agreement,
+
+   2. a notice relating to the limitation of both the Licensor's
+      warranty and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the Object Code of the Software is
+redistributed, the Licensee allows future Licensees unhindered access to
+the full Source Code of the Software by indicating how to access it, it
+being understood that the additional cost of acquiring the Source Code
+shall not exceed the cost of transferring the data.
+
+
+        5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+
+When the Licensee makes a Contribution to the Software, the terms and
+conditions for the distribution of the resulting Modified Software
+become subject to all the provisions of this Agreement.
+
+The Licensee is authorized to distribute the Modified Software, in
+source code or object code form, provided that said distribution
+complies with all the provisions of the Agreement and is accompanied by:
+
+   1. a copy of the Agreement,
+
+   2. a notice relating to the limitation of both the Licensor's
+      warranty and liability as set forth in Articles 8 and 9,
+
+and that, in the event that only the object code of the Modified
+Software is redistributed, the Licensee allows future Licensees
+unhindered access to the full source code of the Modified Software by
+indicating how to access it, it being understood that the additional
+cost of acquiring the source code shall not exceed the cost of
+transferring the data.
+
+
+        5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+
+When the Licensee has developed an External Module, the terms and
+conditions of this Agreement do not apply to said External Module, that
+may be distributed under a separate license agreement.
+
+
+        5.3.4 COMPATIBILITY WITH THE GNU GPL
+
+The Licensee can include a code that is subject to the provisions of one
+of the versions of the GNU GPL in the Modified or unmodified Software,
+and distribute that entire code under the terms of the same version of
+the GNU GPL.
+
+The Licensee can include the Modified or unmodified Software in a code
+that is subject to the provisions of one of the versions of the GNU GPL,
+and distribute that entire code under the terms of the same version of
+the GNU GPL.
+
+
+    Article 6 - INTELLECTUAL PROPERTY
+
+
+      6.1 OVER THE INITIAL SOFTWARE
+
+The Holder owns the economic rights over the Initial Software. Any or
+all use of the Initial Software is subject to compliance with the terms
+and conditions under which the Holder has elected to distribute its work
+and no one shall be entitled to modify the terms and conditions for the
+distribution of said Initial Software.
+
+The Holder undertakes that the Initial Software will remain ruled at
+least by this Agreement, for the duration set forth in Article 4.2.
+
+
+      6.2 OVER THE CONTRIBUTIONS
+
+The Licensee who develops a Contribution is the owner of the
+intellectual property rights over this Contribution as defined by
+applicable law.
+
+
+      6.3 OVER THE EXTERNAL MODULES
+
+The Licensee who develops an External Module is the owner of the
+intellectual property rights over this External Module as defined by
+applicable law and is free to choose the type of agreement that shall
+govern its distribution.
+
+
+      6.4 JOINT PROVISIONS
+
+The Licensee expressly undertakes:
+
+   1. not to remove, or modify, in any manner, the intellectual property
+      notices attached to the Software;
+
+   2. to reproduce said notices, in an identical manner, in the copies
+      of the Software modified or not.
+
+The Licensee undertakes not to directly or indirectly infringe the
+intellectual property rights of the Holder and/or Contributors on the
+Software and to take, where applicable, vis-à-vis its staff, any and all
+measures required to ensure respect of said intellectual property rights
+of the Holder and/or Contributors.
+
+
+    Article 7 - RELATED SERVICES
+
+7.1 Under no circumstances shall the Agreement oblige the Licensor to
+provide technical assistance or maintenance services for the Software.
+
+However, the Licensor is entitled to offer this type of services. The
+terms and conditions of such technical assistance, and/or such
+maintenance, shall be set forth in a separate instrument. Only the
+Licensor offering said maintenance and/or technical assistance services
+shall incur liability therefor.
+
+7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+its sole responsibility, a warranty, that shall only be binding upon
+itself, for the redistribution of the Software and/or the Modified
+Software, under terms and conditions that it is free to decide. Said
+warranty, and the financial terms and conditions of its application,
+shall be subject of a separate instrument executed between the Licensor
+and the Licensee.
+
+
+    Article 8 - LIABILITY
+
+8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+entitled to claim compensation for any direct loss it may have suffered
+from the Software as a result of a fault on the part of the relevant
+Licensor, subject to providing evidence thereof.
+
+8.2 The Licensor's liability is limited to the commitments made under
+this Agreement and shall not be incurred as a result of in particular:
+(i) loss due the Licensee's total or partial failure to fulfill its
+obligations, (ii) direct or consequential loss that is suffered by the
+Licensee due to the use or performance of the Software, and (iii) more
+generally, any consequential loss. In particular the Parties expressly
+agree that any or all pecuniary or business loss (i.e. loss of data,
+loss of profits, operating loss, loss of customers or orders,
+opportunity cost, any disturbance to business activities) or any or all
+legal proceedings instituted against the Licensee by a third party,
+shall constitute consequential loss and shall not provide entitlement to
+any or all compensation from the Licensor.
+
+
+    Article 9 - WARRANTY
+
+9.1 The Licensee acknowledges that the scientific and technical
+state-of-the-art when the Software was distributed did not enable all
+possible uses to be tested and verified, nor for the presence of
+possible defects to be detected. In this respect, the Licensee's
+attention has been drawn to the risks associated with loading, using,
+modifying and/or developing and reproducing the Software which are
+reserved for experienced users.
+
+The Licensee shall be responsible for verifying, by any or all means,
+the suitability of the product for its requirements, its good working
+order, and for ensuring that it shall not cause damage to either persons
+or properties.
+
+9.2 The Licensor hereby represents, in good faith, that it is entitled
+to grant all the rights over the Software (including in particular the
+rights set forth in Article 5).
+
+9.3 The Licensee acknowledges that the Software is supplied "as is" by
+the Licensor without any other express or tacit warranty, other than
+that provided for in Article 9.2 and, in particular, without any warranty 
+as to its commercial value, its secured, safe, innovative or relevant
+nature.
+
+Specifically, the Licensor does not warrant that the Software is free
+from any error, that it will operate without interruption, that it will
+be compatible with the Licensee's own equipment and software
+configuration, nor that it will meet the Licensee's requirements.
+
+9.4 The Licensor does not either expressly or tacitly warrant that the
+Software does not infringe any third party intellectual property right
+relating to a patent, software or any other property right. Therefore,
+the Licensor disclaims any and all liability towards the Licensee
+arising out of any or all proceedings for infringement that may be
+instituted in respect of the use, modification and redistribution of the
+Software. Nevertheless, should such proceedings be instituted against
+the Licensee, the Licensor shall provide it with technical and legal
+assistance for its defense. Such technical and legal assistance shall be
+decided on a case-by-case basis between the relevant Licensor and the
+Licensee pursuant to a memorandum of understanding. The Licensor
+disclaims any and all liability as regards the Licensee's use of the
+name of the Software. No warranty is given as regards the existence of
+prior rights over the name of the Software or as regards the existence
+of a trademark.
+
+
+    Article 10 - TERMINATION
+
+10.1 In the event of a breach by the Licensee of its obligations
+hereunder, the Licensor may automatically terminate this Agreement
+thirty (30) days after notice has been sent to the Licensee and has
+remained ineffective.
+
+10.2 A Licensee whose Agreement is terminated shall no longer be
+authorized to use, modify or distribute the Software. However, any
+licenses that it may have granted prior to termination of the Agreement
+shall remain valid subject to their having been granted in compliance
+with the terms and conditions hereof.
+
+
+    Article 11 - MISCELLANEOUS
+
+
+      11.1 EXCUSABLE EVENTS
+
+Neither Party shall be liable for any or all delay, or failure to
+perform the Agreement, that may be attributable to an event of force
+majeure, an act of God or an outside cause, such as defective
+functioning or interruptions of the electricity or telecommunications
+networks, network paralysis following a virus attack, intervention by
+government authorities, natural disasters, water damage, earthquakes,
+fire, explosions, strikes and labor unrest, war, etc.
+
+11.2 Any failure by either Party, on one or more occasions, to invoke
+one or more of the provisions hereof, shall under no circumstances be
+interpreted as being a waiver by the interested Party of its right to
+invoke said provision(s) subsequently.
+
+11.3 The Agreement cancels and replaces any or all previous agreements,
+whether written or oral, between the Parties and having the same
+purpose, and constitutes the entirety of the agreement between said
+Parties concerning said purpose. No supplement or modification to the
+terms and conditions hereof shall be effective as between the Parties
+unless it is made in writing and signed by their duly authorized
+representatives.
+
+11.4 In the event that one or more of the provisions hereof were to
+conflict with a current or future applicable act or legislative text,
+said act or legislative text shall prevail, and the Parties shall make
+the necessary amendments so as to comply with said act or legislative
+text. All other provisions shall remain effective. Similarly, invalidity
+of a provision of the Agreement, for any reason whatsoever, shall not
+cause the Agreement as a whole to be invalid.
+
+
+      11.5 LANGUAGE
+
+The Agreement is drafted in both French and English and both versions
+are deemed authentic.
+
+
+    Article 12 - NEW VERSIONS OF THE AGREEMENT
+
+12.1 Any person is authorized to duplicate and distribute copies of this
+Agreement.
+
+12.2 So as to ensure coherence, the wording of this Agreement is
+protected and may only be modified by the authors of the License, who
+reserve the right to periodically publish updates or new versions of the
+Agreement, each with a separate number. These subsequent versions may
+address new issues encountered by Free Software.
+
+12.3 Any Software distributed under a given version of the Agreement may
+only be subsequently distributed under the same version of the Agreement
+or a subsequent version, subject to the provisions of Article 5.3.4.
+
+
+    Article 13 - GOVERNING LAW AND JURISDICTION
+
+13.1 The Agreement is governed by French law. The Parties agree to
+endeavor to seek an amicable solution to any disagreements or disputes
+that may arise during the performance of the Agreement.
+
+13.2 Failing an amicable solution within two (2) months as from their
+occurrence, and unless emergency proceedings are necessary, the
+disagreements or disputes shall be referred to the Paris Courts having
+jurisdiction, by the more diligent Party.
+
+
+Version 2.0 dated 2006-09-05.

MANIFEST.in

@@ -0,0 +1,169 @@
+include  .gitignore
+include  CMakeLists.txt
+include  FindNumPy.cmake
+include  FindPyLibs.cmake
+include  GetGitRevisionDescription.cmake
+include  GetGitRevisionDescription.cmake.in
+include  LICENCE.txt
+include  LICENCE_CeCILL_V2
+include  README.md
+include  build_tools/gather_sources.py
+include  color_msg.cmake
+include  doc/Makefile
+include  doc/make.bat
+include  doc/source/conf.py
+include  doc/source/cpplibrary.rst
+include  doc/source/index.rst
+include  doc/source/intro.rst
+include  doc/source/pythonmodule.rst
+include  external/external_build.cmake
+include  external/libsharp-6077806.tar.gz
+include  external/omptl-20120422.tar.bz2
+include  external/patch-omptl
+include  python/CMakeLists.txt
+include  python/_cosmo_bispectrum.cpp
+include  python/_cosmo_cic.pyx
+include  python/_cosmo_power.pyx
+include  python/_cosmotool.pyx
+include  python/_fast_interp.pyx
+include  python/_project.pyx
+include  python/copy.pxd
+include  python/cosmotool/__init__.py
+include  python/cosmotool/bispectrum.py
+include  python/cosmotool/borg.py
+include  python/cosmotool/cic.py
+include  python/cosmotool/cl_cic.py
+include  python/cosmotool/config.py.in
+include  python/cosmotool/ctpv.py
+include  python/cosmotool/fftw.py
+include  python/cosmotool/grafic.py
+include  python/cosmotool/simu.py
+include  python/cosmotool/smooth.py
+include  python/cosmotool/timing.py
+include  python/cppHelper.hpp
+include  python/dummy.c
+include  python/project_tool.hpp
+include  python/safe_gadget.hpp
+include  python_sample/build_2lpt_ksz.py
+include  python_sample/build_2lpt_skymap.py
+include  python_sample/build_dipole_ksz_from_galaxies.py
+include  python_sample/build_nbody_ksz.py
+include  python_sample/build_nbody_ksz_from_galaxies.py
+include  python_sample/build_nbody_skymap.py
+include  python_sample/gen_2lpt_asmooth.py
+include  python_sample/gen_2lpt_density.py
+include  python_sample/icgen/__init__.py
+include  python_sample/icgen/borgadaptor.py
+include  python_sample/icgen/borgicgen.py
+include  python_sample/icgen/cosmogrowth.py
+include  python_sample/icgen/gen_ic_from_borg.py
+include  python_sample/icgen/test_ic_from_borg.py
+include  python_sample/icgen/test_whitify.py
+include  python_sample/ksz/__init__.py
+include  python_sample/ksz/constants.py
+include  python_sample/ksz/gal_prof.py
+include  python_sample/ramsesToArray.py
+include  python_sample/test_bispectrum.py
+include  python_sample/test_spheric_proj.py
+include  sample/CMakeLists.txt
+include  sample/Hartmann_Matrix.txt
+include  sample/gadgetToArray.cpp
+include  sample/gadgetToDensity.cpp
+include  sample/graficToDensity.cpp
+include  sample/simple3DFilter.cpp
+include  sample/simpleDistanceFilter.cpp
+include  sample/testAlgo.cpp
+include  sample/testBQueue.cpp
+include  sample/testBSP.cpp
+include  sample/testDelaunay.cpp
+include  sample/testEskow.cpp
+include  sample/testHDF5.cpp
+include  sample/testInterpolate.cpp
+include  sample/testNewton.cpp
+include  sample/testPool.cpp
+include  sample/testReadFlash.cpp
+include  sample/testSmooth.cpp
+include  sample/test_cosmopower.cpp
+include  sample/test_fft_calls.cpp
+include  sample/test_healpix_calls.cpp
+include  sample/testkd.cpp
+include  sample/testkd2.cpp
+include  sample/testkd3.cpp
+include  setup.py
+include  src/CMakeLists.txt
+include  src/algo.hpp
+include  src/bqueue.hpp
+include  src/bqueue.tcc
+include  src/bsp_simple.hpp
+include  src/bsp_simple.tcc
+include  src/cic.cpp
+include  src/cic.hpp
+include  src/config.hpp
+include  src/cosmopower.cpp
+include  src/cosmopower.hpp
+include  src/dinterpolate.hpp
+include  src/dinterpolate.tcc
+include  src/eskow.hpp
+include  src/field.hpp
+include  src/fixArray.hpp
+include  src/fortran.cpp
+include  src/fortran.hpp
+include  src/fourier/base_types.hpp
+include  src/fourier/details/euclidian_maps.hpp
+include  src/fourier/details/euclidian_spectrum_1d.hpp
+include  src/fourier/details/euclidian_spectrum_1d_bin.hpp
+include  src/fourier/details/euclidian_transform.hpp
+include  src/fourier/details/healpix_alms.hpp
+include  src/fourier/details/healpix_map.hpp
+include  src/fourier/details/healpix_spectrum.hpp
+include  src/fourier/details/healpix_transform.hpp
+include  src/fourier/details/healpix_utility.hpp
+include  src/fourier/euclidian.hpp
+include  src/fourier/fft/fftw_calls.hpp
+include  src/fourier/fft/fftw_calls_mpi.hpp
+include  src/fourier/fft/fftw_complex.hpp
+include  src/fourier/healpix.hpp
+include  src/growthFactor.cpp
+include  src/growthFactor.hpp
+include  src/h5_readFlash.cpp
+include  src/h5_readFlash.hpp
+include  src/hdf5_array.hpp
+include  src/hdf5_flash.h
+include  src/interpolate.cpp
+include  src/interpolate.hpp
+include  src/interpolate3d.hpp
+include  src/kdtree_leaf.hpp
+include  src/kdtree_leaf.tcc
+include  src/kdtree_splitters.hpp
+include  src/loadFlash.cpp
+include  src/loadFlash.hpp
+include  src/loadFlash_dummy.cpp
+include  src/loadGadget.cpp
+include  src/loadGadget.hpp
+include  src/loadRamses.cpp
+include  src/loadRamses.hpp
+include  src/loadSimu.hpp
+include  src/load_data.cpp
+include  src/load_data.hpp
+include  src/mach.hpp
+include  src/miniargs.cpp
+include  src/miniargs.hpp
+include  src/mykdtree.hpp
+include  src/mykdtree.tcc
+include  src/newton.hpp
+include  src/octTree.hpp
+include  src/octTree.tcc
+include  src/openmp.hpp
+include  src/pool.hpp
+include  src/powerSpectrum.cpp
+include  src/powerSpectrum.hpp
+include  src/replicateGenerator.hpp
+include  src/sparseGrid.hpp
+include  src/sparseGrid.tcc
+include  src/sphSmooth.hpp
+include  src/sphSmooth.tcc
+include  src/symbol_visible.hpp
+include  src/tf_fit.hpp
+include  src/yorick.hpp
+include  src/yorick_nc3.cpp
+include  src/yorick_nc4.cpp

builder/build-wheels.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+set -e -x
+
+CC=cc
+CXX=c++
+
+export CC CXX
+
+# Install a system package required by our library
+#yum install -y atlas-devel
+yum install -y cmake3 gsl-devel zlib-devel
+
+ln -fs /usr/bin/cmake3 /usr/bin/cmake
+
+
+ALL_PYTHON="cp36-cp36m cp37-cp37m cp38-cp38 cp39-cp39" 
+
+# Compile wheels
+for pkg in $ALL_PYTHON; do
+    PYBIN=/opt/python/${pkg}/bin
+#    "${PYBIN}/pip" install -r /io/dev-requirements.txt
+    "${PYBIN}/pip" install -r /io/requirements.txt
+    "${PYBIN}/pip" wheel -vvv /io/ -w wheelhouse/
+done
+
+# Bundle external shared libraries into the wheels
+for whl in wheelhouse/*.whl; do
+    auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/
+done
+
+# Install packages and test
+for pkg in $ALL_PYTHON; do
+    PYBIN=/opt/python/${pkg}/bin
+    "${PYBIN}/pip" install cosmotool --no-index -f /io/wheelhouse
+done

builder/start.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+d=$(pwd)
+if test x"$(basename $d)" = xbuilder; then
+  d=${d}/../
+fi
+if ! [ -e ${d}/setup.py ] ; then
+  echo "Unknown directory. Please move to the root of cosmotool source tree."
+  exit 1
+fi
+
+podman run -ti  --rm -e PLAT=manylinux2010_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2010_x86_64 /io/builder/build-wheels.sh

conda/build.sh

@@ -0,0 +1 @@
+$PYTHON setup.py install

conda/conda_build_config.yaml

@@ -0,0 +1,7 @@
+python:
+  - 3.7
+  - 3.8
+
+numpy:
+  - 1.11
+  - 1.19

conda/meta.yaml

@@ -0,0 +1,38 @@
+package:
+  name: cosmotool
+  version: "1.0.0a7"
+
+source:
+  git_rev: 7fce73e
+  git_url: https://bitbucket.org/glavaux/cosmotool
+
+requirements:
+  build:
+    - numpy >=1.11
+    - gcc_linux-64
+    - gxx_linux-64
+    - python
+    - setuptools
+    - cython
+    - healpy
+    - numexpr
+    - cffi
+    - pyfftw
+    - gsl
+    - h5py
+
+  run:
+    - numpy
+    - python
+    - healpy
+    - numexpr
+    - cffi
+    - pyfftw
+    - h5py
+
+test:
+  imports:
+    - cosmotool
+
+about:
+  home: https://bitbucket.org/glavaux/cosmotool

external/external_build.cmake

@@ -2,8 +2,8 @@ include(FindOpenMP)
 
 OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
 
-SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE URL "URL to download FFTW from")
+SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE STRING "URL to download FFTW from")
-SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz" CACHE URL "URL to download Eigen from")
+SET(EIGEN_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2" CACHE STRING "URL to download Eigen from")
 SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from")
 SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.bz2" CACHE STRING "URL to download HDF5 from")
 SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz" CACHE STRING "URL to download NetCDF from")
@@ -56,19 +56,19 @@ if (ENABLE_SHARP)
   IF(NOT ENABLE_OPENMP)
     SET(SHARP_OPENMP --disable-openmp)
   ENDIF()
-  ExternalProject_Add(sharp
-    URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz
-    PREFIX ${BUILD_PREFIX}/sharp-prefix
-    BUILD_IN_SOURCE 1 
-    CONFIGURE_COMMAND autoconf && ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP}
-    BUILD_COMMAND ${CMAKE_MAKE_PROGRAM}
-    INSTALL_COMMAND echo "No install"
-  )
   SET(CUTILS_LIBRARY ${DEP_BUILD}/lib/libc_utils.a)
   SET(FFTPACK_LIBRARY ${DEP_BUILD}/lib/libfftpack.a)
   SET(SHARP_LIBRARY ${DEP_BUILD}/lib/libsharp.a)
   SET(SHARP_LIBRARIES ${SHARP_LIBRARY} ${FFTPACK_LIBRARY} ${CUTILS_LIBRARY})
   SET(SHARP_INCLUDE_PATH ${DEP_BUILD}/include)
+  ExternalProject_Add(sharp
+    URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz
+    PREFIX ${BUILD_PREFIX}/sharp-prefix
+    BUILD_IN_SOURCE 1 
+    CONFIGURE_COMMAND autoconf && ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP}
+    INSTALL_COMMAND echo "No install"
+    BUILD_BYPRODUCTS ${SHARP_LIBRARIES}
+  )
 endif (ENABLE_SHARP)
 
 
@@ -246,10 +246,23 @@ if (INTERNAL_BOOST)
   set(Boost_DEP boost)
 
 ELSE (INTERNAL_BOOST)
-  find_package(Boost 1.53 QUIET)
+  find_package(Boost 1.69 QUIET)
-  set(Boost_DEP)
+  if (Boost_VERSION)
+    if (${Boost_VERSION} VERSION_GREATER 1000)
+       math(EXPR TMP_MAJOR "${Boost_VERSION} / 100000")
+       math(EXPR TMP_MINOR "(${Boost_VERSION} - ${TMP_MAJOR} * 100000) / 100")
+       math(EXPR TMP_PATCHLEVEL "${Boost_VERSION} - ${TMP_MAJOR} * 100000 - ${TMP_MINOR} * 100")
+       set(Boost_VERSION ${TMP_MAJOR}.${TMP_MINOR}.${TMP_PATCHLEVEL})
+    ENDIF()
+    if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0)
+      set(Boost_DEP Boost::boost)
+      set(Boost_TARGET Boost::boost)
+    endif()
+  endif()
   if (NOT Boost_FOUND)
-    cmessage(CWARNING "Boost >= 1.53 was not found")
+    cmessage(CWARNING "Boost >= 1.69 was not found")
+  else()
+    cmessage(STATUS "Boost has been found (version=${Boost_VERSION}), Boost_TARGET=${Boost_Target}")
   endif()
 endif (INTERNAL_BOOST)
 mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES)
@@ -278,13 +291,19 @@ IF(INTERNAL_GSL)
   set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
   SET(cosmotool_DEPS ${cosmotool_DEPS} gsl)
 ELSE(INTERNAL_GSL)
-  find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
+  IF (NOT DEFINED GSL_LIBRARY OR NOT GSL_LIBRARY)
-  find_library(GSL_LIBRARY gsl)
+    find_library(GSL_LIBRARY gsl)
-  find_library(GSLCBLAS_LIBRARY gslcblas)
+  ENDIF()
+  IF (NOT DEFINED GSL_INCLUDE_PATH OR NOT GSL_INCLUDE_PATH)
+    find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
+  ENDIF()
+  IF (NOT DEFINED GSL_CBLAS_LIBRARY OR NOT GSL_CBLAS_LIBRARY)
+    find_library(GSLCBLAS_LIBRARY gslcblas)
+  ENDIF()
 
   set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
-
 ENDIF(INTERNAL_GSL)
+
 mark_as_advanced(GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
 
 
@@ -337,7 +356,7 @@ ENDIF(INTERNAL_FFTW)
 IF (INTERNAL_EIGEN)
   ExternalProject_Add(eigen
      URL ${EIGEN_URL}
-     URL_HASH SHA256=04f8a4fa4afedaae721c1a1c756afeea20d3cdef0ce3293982cf1c518f178502 
+     URL_HASH MD5=b9e98a200d2455f06db9c661c5610496
      PREFIX ${BUILD_PREFIX}/eigen-prefix
      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
        -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
@@ -375,6 +394,7 @@ ExternalProject_Add(omptl
   BUILD_COMMAND echo "No build"
   PATCH_COMMAND patch -p1 -t -N < ${CMAKE_SOURCE_DIR}/external/patch-omptl
   INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${OMPTL_BUILD_DIR} ${EXT_INSTALL}/include/omptl
+  BUILD_BYPRODUCTS ${EXT_INSTALL}/include/omptl
 )
 include_directories(${EXT_INSTALL}/include)
 ##include_directories(${OMPTL_BUILD_DIR}/src/)

python/CMakeLists.txt

@@ -30,6 +30,10 @@ IF(CYTHON)
     COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx
     DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx ${CMAKE_CURRENT_SOURCE_DIR}/project_tool.hpp ) 
 
+  add_custom_command(
+    OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp
+    COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmomath.pyx
+    DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmomath.pyx ) 
 ENDIF(CYTHON)
 
 
@@ -38,25 +42,27 @@ add_library(_cosmo_power MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp)
 add_library(_cosmo_cic MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp)
 add_library(_fast_interp MODULE ${CMAKE_CURRENT_BINARY_DIR}/_fast_interp.cpp)
 add_library(_project MODULE ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp)
+add_library(_cosmomath MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp)
 target_include_directories(_cosmotool PRIVATE ${PYTHON_INCLUDES}) 
 target_include_directories(_cosmo_power PRIVATE ${PYTHON_INCLUDES}) 
 target_include_directories(_cosmo_cic PRIVATE ${PYTHON_INCLUDES}) 
 target_include_directories(_fast_interp PRIVATE ${PYTHON_INCLUDES}) 
 target_include_directories(_project PRIVATE ${PYTHON_INCLUDES}) 
-
+target_include_directories(_cosmomath PRIVATE ${PYTHON_INCLUDES})
 
 SET(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -Bsymbolic-functions")
 if(APPLE)
   set(CMAKE_MODULE_LINKER_FLAGS "-undefined dynamic_lookup")
 endif()
 
-target_link_libraries(_cosmotool ${CosmoTool_local}  ${GSL_LIBRARIES})
+target_link_libraries(_cosmotool PRIVATE ${CosmoTool_local}  ${GSL_LIBRARIES})
-target_link_libraries(_cosmo_power ${CosmoTool_local} ${GSL_LIBRARIES})
+target_link_libraries(_cosmo_power PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES})
-target_link_libraries(_cosmo_cic ${CosmoTool_local}  ${GSL_LIBRARIES})
+target_link_libraries(_cosmo_cic PRIVATE ${CosmoTool_local}  ${GSL_LIBRARIES})
+target_link_libraries(_cosmomath PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES})
 target_link_libraries(_project )
-target_link_libraries(_fast_interp ${CosmoTool_local} )
+target_link_libraries(_fast_interp PRIVATE ${CosmoTool_local} )
 
-SET(ct_TARGETS   _cosmotool _project _cosmo_power _cosmo_cic _fast_interp )
+SET(ct_TARGETS   _cosmotool _project _cosmo_power _cosmo_cic _fast_interp _cosmomath)
 
 if (Boost_FOUND)
   message(STATUS "Building bispectrum support (path = ${Boost_INCLUDE_DIRS})")

python/_cosmomath.pyx

@@ -0,0 +1,45 @@
+#cython: language_level=3
+import numpy as np
+cimport numpy as np
+
+np.import_array()
+np.import_ufunc()
+
+cdef extern from "sys/types.h":
+   ctypedef np.int64_t int64_t
+
+cdef extern from "numpy/npy_common.h":
+   ctypedef npy_intp
+
+cdef extern from "special_math.hpp" namespace "CosmoTool":
+   T log_modified_bessel_first_kind[T](T v, T z) nogil except +
+
+cdef extern from "numpy_adaptors.hpp" namespace "CosmoTool":
+   void parallel_ufunc_dd_d[T,IT](char **args, IT* dimensions, IT* steps, void *func)
+
+
+cdef np.PyUFuncGenericFunction loop_func[1]
+cdef char input_output_types[3]
+cdef void *elementwise_funcs[1]
+
+loop_func[0] = <np.PyUFuncGenericFunction>parallel_ufunc_dd_d[double,npy_intp]
+
+input_output_types[0] = np.NPY_DOUBLE
+input_output_types[1] = np.NPY_DOUBLE
+input_output_types[2] = np.NPY_DOUBLE
+
+elementwise_funcs[0] = <void*>log_modified_bessel_first_kind[double]
+
+log_modified_I = np.PyUFunc_FromFuncAndData(
+    loop_func,
+    elementwise_funcs,
+    input_output_types,
+    1, # number of supported input types
+    2, # number of input args
+    1, # number of output args
+    0, # `identity` element, never mind this
+    "log_modified_bessel_first_kind", # function name
+    "log_modified_bessel_first_kind(v: Float, z: Float) -> Float", # docstring
+    0 # unused
+    )
+

python/_cosmotool.pyx

@@ -513,7 +513,8 @@ def writeGadget(str filename, object simulation):
   simdata.TotalNumPart = NumPart
   simdata.NumPart = NumPart
 
-  cxx_writeGadget(filename, &simdata)
+  filename_b = bytes(filename, 'utf-8')
+  cxx_writeGadget(filename_b, &simdata)
 
 def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = False, bool loadPosition = True, bool loadVelocity = False, bool loadId = False, bool loadMass = False):
   """ loadRamses(basepath, snapshot_id, cpu_id, doublePrecision = False, loadPosition = True, loadVelocity = False)

python/cosmotool/__init__.py

@@ -3,6 +3,7 @@ from ._project import *
 from ._cosmo_power import *
 from ._cosmo_cic import *
 from ._fast_interp import *
+from ._cosmomath import *
 from .grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
 from .borg import read_borg_vol
 from .cic import cicParticles

python/cosmotool/ctpv.py

@@ -87,7 +87,7 @@ class ProgrammableParticleHistoryLoad(object):
 class ProgrammableDensityLoad(object):
 
   @staticmethod
-  def main_script(source, density, extents=None, aname="default"):
+  def main_script(source, density, extents=None, aname="default", extra_arrays={}):
     import vtk
     from vtk.util import numpy_support
   
@@ -116,6 +116,11 @@ class ProgrammableDensityLoad(object):
        arr = numpy_support.numpy_to_vtk(density.transpose().astype(np.float64).ravel(), deep=1)
     arr.SetName(aname)
     ido.GetPointData().AddArray(arr)
+
+    for k in extra_arrays.keys():
+        arr = numpy_support.numpy_to_vtk(extra_arrays[k].transpose().astype(np.float64).ravel(), deep=1)
+        arr.SetName(k)
+        ido.GetPointData().AddArray(arr)
     
   @staticmethod
   def request_information(source, density=None, dims=None):

python/cosmotool/simu.py

@@ -98,12 +98,12 @@ def simpleWriteGadget(filename, positions, boxsize=1.0, Hubble=100, Omega_M=0.30
   
   s.positions = positions
   
-  if velocities:
+  if velocities is not None:
     s.velocities = velocities
   else:
     s.velocities = [np.zeros(positions[0].size,dtype=np.float32)]*3
     
-  if identifiers:
+  if identifiers is not None:
     s.identifiers = identifiers
   else:
     s.identifiers = np.arange(positions[0].size, dtype=np.int64)

python/dummy.c

@@ -0,0 +1 @@
+static void dummyFunc() {}

requirements.txt

@@ -0,0 +1,5 @@
+numpy
+cffi
+numexpr
+pyfftw
+cython

sample/CMakeLists.txt

@@ -114,6 +114,9 @@ if (Boost_FOUND)
       add_dependencies(graficToDensity ${all_deps})
     endif()
   endif()
+
+  add_executable(test_special test_special.cpp)
+  target_link_libraries(test_special ${tolink})
 endif (Boost_FOUND)
 
 IF (ENABLE_OPENMP AND YORICK_SUPPORT)

sample/test_special.cpp

@@ -0,0 +1,12 @@
+#include <iostream>
+#include "special_math.hpp"
+
+int main()
+{
+
+    std::cout << CosmoTool::log1p_exp(2.0) << std::endl;
+
+    std::cout << CosmoTool::log_modified_bessel_first_kind(100.0, 0.1) << std::endl;
+    return 0;
+}
+    

setup.py

@@ -21,7 +21,7 @@ class CMakeExtension(Extension):
     doesn't try to build your sources for you
     """
 
-    def __init__(self, name, sources=[]):
+    def __init__(self, name, sources=["python/dummy.c"]):
 
         super().__init__(name = name, sources = sources)
 
@@ -156,9 +156,8 @@ class BuildCMakeExt(build_ext):
 
         cython_code = os.path.join(str(build_dir.absolute()),'mycython')
         with open(cython_code, mode="wt") as ff:
-          ff.write(f"#!{sys.executable}\n"
+          ff.write("#!/bin/sh\n"
-                    "from Cython.Compiler.Main import setuptools_main\n"
+                   f"{sys.executable} -c 'from Cython.Compiler.Main import setuptools_main; setuptools_main()' $@")
-                    "setuptools_main()")
         os.chmod(cython_code, stat.S_IXUSR|stat.S_IWUSR|stat.S_IRUSR|stat.S_IRGRP)
 
         # Now that the necessary directories are created, build
@@ -169,6 +168,7 @@ class BuildCMakeExt(build_ext):
         # Below is just an example set of arguments for building Blender as a Python module
 
         self.spawn(['cmake', '-H'+SOURCE_DIR, '-B'+self.build_temp,
+                    '-DCMAKE_C_COMPILER=' + os.environ["CC"], "-DCMAKE_CXX_COMPILER=" + os.environ["CXX"],
                     '-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON',
                     '-DINTERNAL_HDF5=ON','-DINTERNAL_NETCDF=ON',
                     '-DBUILD_PYTHON=ON', '-DINSTALL_PYTHON_LOCAL=OFF',
@@ -218,10 +218,11 @@ class BuildCMakeExt(build_ext):
 CosmoTool_extension = CMakeExtension(name="cosmotool")
 
 setup(name='cosmotool',
-      version='1.0.0a2',
+      version='1.1.1',
       packages=["cosmotool"],
       package_dir={'cosmotool': 'python/cosmotool'},
-      setup_requires=['cython','cffi','numexpr'],
+      install_requires=['numpy','cffi','numexpr','pyfftw','h5py'],
+      setup_requires=['cython','cffi','numpy','numexpr'],
       ext_modules=[CosmoTool_extension],
       description='A small cosmotool box of useful functions',
       long_description=open("./README.md", 'r').read(),
@@ -241,5 +242,6 @@ setup(name='cosmotool',
           'build_ext': BuildCMakeExt,
           'install_data': InstallCMakeLibsData,
           'install_lib': InstallCMakeLibs,
-          }
+          },
+      python_requires='>=3.6'
 )

src/CMakeLists.txt

@@ -72,14 +72,14 @@ SET(CosmoTool_SRCS ${CosmoTool_SRCS}
 
 include_directories(${GSL_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
 
-set(CosmoTool_LIBS ${GSL_LIBRARIES})
+set(CosmoTool_LIBS ${GSL_LIBRARIES} ${Boost_TARGET})
 if(YORICK_SUPPORT)
   set(CosmoTool_LIBS ${CosmoTool_LIBS} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
   include_directories(${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH})
 endif(YORICK_SUPPORT)
 
 if (HDF5_FOUND)
-  set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${ZLIB})
+  set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${ZLIB_LIBRARY})
   message(STATUS "CosmoTool_LIBS: ${CosmoTool_LIBS}")
 endif (HDF5_FOUND)
 
@@ -92,11 +92,13 @@ if (BUILD_SHARED_LIBS)
      add_library(CosmoTool_static STATIC ${CosmoTool_SRCS} $<TARGET_OBJECTS:CosmoHDF5>)
      target_link_libraries(CosmoTool_static)
      set_property(TARGET CosmoTool_static PROPERTY POSITION_INDEPENDENT_CODE ON)
+     add_dependencies(CosmoTool_static ${cosmotool_DEPS})
   endif(BUILD_STATIC_LIBS)
 else (BUILD_SHARED_LIBS)
   add_library(CosmoTool STATIC ${CosmoTool_SRCS} $<TARGET_OBJECTS:CosmoHDF5>)
-  target_link_libraries(CosmoTool)
+  target_link_libraries(CosmoTool ${CosmoTool_LIBS})
   set_property(TARGET CosmoTool PROPERTY POSITION_INDEPENDENT_CODE ON)
+  add_dependencies(CosmoTool ${cosmotool_DEPS})
 endif (BUILD_SHARED_LIBS)
 
 IF(NOT COSMOTOOL_PYTHON_PACKAGING)

src/algo.hpp

@@ -93,6 +93,6 @@ namespace  CosmoTool
 
 
 
-};
+}
 
 #endif

src/config.hpp

@@ -165,6 +165,6 @@ namespace CosmoTool
     FilesystemFullException()
       : Exception() {}
   };
-};
+}
 
 #endif

src/fourier/fft/fftw_calls.hpp

@@ -114,6 +114,9 @@ public: \
   static plan_type plan_dft_3d(int Nx, int Ny, int Nz, complex_type *in, complex_type *out, int sign, unsigned flags) { \
     return prefix ## _plan_dft_3d(Nx, Ny, Nz, in, out, sign, flags); \
   } \
+  static plan_type plan_dft_2d(int Nx, int Ny, complex_type *in, complex_type *out, int sign, unsigned flags) { \
+    return prefix ## _plan_dft_2d(Nx, Ny, in, out, sign, flags); \
+  } \
   static void destroy_plan(plan_type plan) { prefix ## _destroy_plan(plan); } \
 }
 

src/fourier/fft/fftw_calls_mpi.hpp

@@ -97,6 +97,9 @@ public: \
   static plan_type plan_dft_3d(int Nx, int Ny, int Nz, complex_type *in, complex_type *out, MPI_Comm comm, int sign, unsigned flags) { \
     return prefix ## _mpi_plan_dft_3d(Nx, Ny, Nz, in, out, comm, sign, flags); \
   } \
+  static plan_type plan_dft_2d(int Nx, int Ny, complex_type *in, complex_type *out, MPI_Comm comm, int sign, unsigned flags) { \
+    return prefix ## _mpi_plan_dft_2d(Nx, Ny, in, out, comm, sign, flags); \
+  } \
   static void destroy_plan(plan_type plan) { prefix ## _destroy_plan(plan); } \
 }
 

src/hdf5_array.hpp

@@ -78,8 +78,6 @@ namespace CosmoTool {
       }
   };
   
- //, typename boost::enable_if<boost::is_same<T, tl> >::type>  \
- //
   #define HDF5_TYPE(tl, thdf5) \
   template<typename T> struct get_hdf5_data_type<T, typename boost::enable_if<boost::is_same<T,tl> >::type > \
     { static H5::DataType type() { return H5::PredType::thdf5; }; }
@@ -122,7 +120,7 @@ namespace CosmoTool {
 
   template<>
   struct hdf5_extent_gen<0> {    
-    static inline boost::multi_array_types::extent_gen build(hsize_t *d)
+    static inline boost::multi_array_types::extent_gen build(hsize_t *)
     {
       return boost::extents;
     }
@@ -513,7 +511,7 @@ namespace CosmoTool { \
     }; \
 };
 
-};
+}
 
 #endif
 

src/loadRamses.cpp

@@ -34,7 +34,7 @@ knowledge of the CeCILL license and that you accept its terms.
 +*/
 
 #include <sys/types.h>
-#include "/usr/include/regex.h"
+#include <regex.h>
 #include <cmath>
 #include <cstring>
 #include <cstdlib>

src/numpy_adaptors.hpp

@@ -0,0 +1,30 @@
+#ifndef __COSMOTOOL_NUMPY_ADAPTOR_HPP
+#define __COSMOTOOL_NUMPY_ADAPTOR_HPP
+
+namespace CosmoTool {
+
+  template<typename T, typename IT>
+  void parallel_ufunc_dd_d(char **args, IT* dimensions, IT* steps, void *func) {
+    IT i;
+    IT n = dimensions[0];
+    char *in = args[0], *in2 = args[1], *out = args[2];
+    IT in_step = steps[0], in2_step = steps[1], out_step = steps[2];
+
+    double tmp;
+    typedef double (*F_t)(double,double);
+
+    F_t f = (F_t)func;
+
+#pragma omp parallel for schedule(static)
+    for (i = 0; i < n; i++) {
+        T *out_t = (T *)(out + i * out_step);
+        T *in_t = (T *)(in + i * in_step);
+        T *in2_t = (T *)(in2 + i * in2_step);
+        *out_t = f(*in_t, *in2_t);
+    }
+  }
+
+
+}
+
+#endif

src/special_math.hpp

@@ -0,0 +1,231 @@
+// Original code derived from Boost and is distributed here
+// under the Boost license (licenses/boost-license.txt)
+//    Copyright (c) 2006 Xiaogang Zhang
+//    Copyright (c) 2007, 2017 John Maddock
+// Secondary code copyright by its author and is distributed here
+// under the BSD-3 license (LICENSE.md). Derived from
+// stan/math/prim/fun/log_modified_bessel_first_kind.hpp
+
+#ifndef __COSMOTOOL_SPECIAL_MATH_HPP
+#define __COSMOTOOL_SPECIAL_MATH_HPP
+
+#include "algo.hpp"
+#include <boost/math/constants/constants.hpp>
+#include <boost/math/tools/rational.hpp>
+#include <cmath>
+#include <limits>
+
+// Taken and adapted from
+// https://github.com/stan-dev/math/blob/develop/stan/math/prim/fun/log_modified_bessel_first_kind.hpp
+
+namespace CosmoTool {
+
+template <typename T> T log1p_exp(T x) {
+  if (x > T(0)) {
+    return x + std::log1p(std::exp(-x));
+  }
+  return std::log1p(std::exp(x));
+}
+
+template <typename T> T multiply_log(T a, T b) {
+  if (a == 0 && b == 0)
+    return 0;
+  return a * std::log(b);
+}
+
+template <typename T> T inf() { return std::numeric_limits<T>::infinity(); }
+
+template <typename T> T log_sum_exp(T const a, T const b) {
+  if (a == -inf<T>()) {
+    return b;
+  }
+  if (a == inf<T>() && b == inf<T>()) {
+    return inf<T>();
+  }
+  if (a > b) {
+    return a + log1p_exp(b - a);
+  }
+  return b + log1p_exp(a - b);
+}
+
+/* Log of the modified Bessel function of the first kind,
+ * which is better known as the Bessel I function. See
+ * modified_bessel_first_kind.hpp for the function definition.
+ * The derivatives are known to be incorrect for v = 0 because a
+ * simple constant 0 is returned.
+ *
+ * @tparam T common type for calculation
+ * @param v Order, can be a non-integer but must be at least -1
+ * @param z Real non-negative number
+ * @throws std::domain_error if either v or z is NaN, z is
+ * negative, or v is less than -1
+ * @return log of Bessel I function
+ */
+template <typename T> T log_modified_bessel_first_kind(T const v, T const z) {
+  using boost::math::tools::evaluate_polynomial;
+  using std::log;
+  using std::pow;
+  using std::sqrt;
+  static const double LOG_TWO = std::log(2.0);
+  static const double EPSILON = std::numeric_limits<double>::epsilon();
+  static const double TWO_PI = 2.0 * boost::math::constants::pi<double>();
+
+  if (z == 0) {
+    if (v == 0) {
+      return 0.0;
+    }
+    if (v > 0) {
+      return -std::numeric_limits<T>::infinity();
+    }
+    return std::numeric_limits<T>::infinity();
+  }
+  if (std::isinf(z)) {
+    return z;
+  }
+  if (v == 0) {
+    // Modified Bessel function of the first kind of order zero
+    // we use the approximating forms derived in:
+    // "Rational Approximations for the Modified Bessel Function of the
+    // First Kind -- I0(x) for Computations with Double Precision"
+    // by Pavel Holoborodko, see
+    // http://www.advanpix.com/2015/11/11/rational-approximations-for-the-modified-bessel-function-of-the-first-kind-i0-computations-double-precision
+    // The actual coefficients used are [Boost's] own, and extend
+    // Pavel's work to precisions other than double.
+
+    if (z < 7.75) {
+      // Bessel I0 over[10 ^ -16, 7.75]
+      // Max error in interpolated form : 3.042e-18
+      // Max Error found at double precision = Poly : 5.106609e-16
+      //                                       Cheb : 5.239199e-16
+      static const double P[] = {
+          1.00000000000000000e+00, 2.49999999999999909e-01,
+          2.77777777777782257e-02, 1.73611111111023792e-03,
+          6.94444444453352521e-05, 1.92901234513219920e-06,
+          3.93675991102510739e-08, 6.15118672704439289e-10,
+          7.59407002058973446e-12, 7.59389793369836367e-14,
+          6.27767773636292611e-16, 4.34709704153272287e-18,
+          2.63417742690109154e-20, 1.13943037744822825e-22,
+          9.07926920085624812e-25};
+      return log1p_exp(multiply_log(2.0, z) - log(4.0) +
+                       log(evaluate_polynomial(P, 0.25 * square(z))));
+    }
+    if (z < 500) {
+      // Max error in interpolated form : 1.685e-16
+      // Max Error found at double precision = Poly : 2.575063e-16
+      //                                       Cheb : 2.247615e+00
+      static const double P[] = {
+          3.98942280401425088e-01,  4.98677850604961985e-02,
+          2.80506233928312623e-02,  2.92211225166047873e-02,
+          4.44207299493659561e-02,  1.30970574605856719e-01,
+          -3.35052280231727022e+00, 2.33025711583514727e+02,
+          -1.13366350697172355e+04, 4.24057674317867331e+05,
+          -1.23157028595698731e+07, 2.80231938155267516e+08,
+          -5.01883999713777929e+09, 7.08029243015109113e+10,
+          -7.84261082124811106e+11, 6.76825737854096565e+12,
+          -4.49034849696138065e+13, 2.24155239966958995e+14,
+          -8.13426467865659318e+14, 2.02391097391687777e+15,
+          -3.08675715295370878e+15, 2.17587543863819074e+15};
+      return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
+    }
+    // Max error in interpolated form : 2.437e-18
+    // Max Error found at double precision = Poly : 1.216719e-16
+    static const double P[] = {3.98942280401432905e-01, 4.98677850491434560e-02,
+                               2.80506308916506102e-02, 2.92179096853915176e-02,
+                               4.53371208762579442e-02};
+    return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
+  }
+  if (v == 1) { // WARNING: will not autodiff for v = 1 correctly
+    // modified from Boost's bessel_i1_imp in the double precision case
+    // see credits above in the v == 0 case
+    if (z < 7.75) {
+      // Bessel I0 over[10 ^ -16, 7.75]
+      // Max error in interpolated form: 5.639e-17
+      // Max Error found at double precision = Poly: 1.795559e-16
+
+      static const double P[] = {
+          8.333333333333333803e-02, 6.944444444444341983e-03,
+          3.472222222225921045e-04, 1.157407407354987232e-05,
+          2.755731926254790268e-07, 4.920949692800671435e-09,
+          6.834657311305621830e-11, 7.593969849687574339e-13,
+          6.904822652741917551e-15, 5.220157095351373194e-17,
+          3.410720494727771276e-19, 1.625212890947171108e-21,
+          1.332898928162290861e-23};
+      T a = square(z) * 0.25;
+      T Q[3] = {1, 0.5, evaluate_polynomial(P, a)};
+      return log(z) + log(evaluate_polynomial(Q, a)) - LOG_TWO;
+    }
+    if (z < 500) {
+      // Max error in interpolated form: 1.796e-16
+      // Max Error found at double precision = Poly: 2.898731e-16
+
+      static const double P[] = {
+          3.989422804014406054e-01,  -1.496033551613111533e-01,
+          -4.675104253598537322e-02, -4.090895951581637791e-02,
+          -5.719036414430205390e-02, -1.528189554374492735e-01,
+          3.458284470977172076e+00,  -2.426181371595021021e+02,
+          1.178785865993440669e+04,  -4.404655582443487334e+05,
+          1.277677779341446497e+07,  -2.903390398236656519e+08,
+          5.192386898222206474e+09,  -7.313784438967834057e+10,
+          8.087824484994859552e+11,  -6.967602516005787001e+12,
+          4.614040809616582764e+13,  -2.298849639457172489e+14,
+          8.325554073334618015e+14,  -2.067285045778906105e+15,
+          3.146401654361325073e+15,  -2.213318202179221945e+15};
+      return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
+    }
+    // Max error in interpolated form: 1.320e-19
+    // Max Error found at double precision = Poly: 7.065357e-17
+    static const double P[] = {
+        3.989422804014314820e-01, -1.496033551467584157e-01,
+        -4.675105322571775911e-02, -4.090421597376992892e-02,
+        -5.843630344778927582e-02};
+    return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
+  }
+  if (z > 100) {
+    // Boost does something like this in asymptotic_bessel_i_large_x
+    T lim = pow((square(v) + 2.5) / (2 * z), 3) / 24;
+    if (lim < (EPSILON * 10)) {
+      T s = 1;
+      T mu = 4 * square(v);
+      T ex = 8 * z;
+      T num = mu - 1;
+      T denom = ex;
+      s -= num / denom;
+      num *= mu - 9;
+      denom *= ex * 2;
+      s += num / denom;
+      num *= mu - 25;
+      denom *= ex * 3;
+      s -= num / denom;
+      s = z - log(sqrt(z * TWO_PI)) + log(s);
+      return s;
+    }
+  }
+
+  T log_half_z = log(0.5 * z);
+  T lgam = (v > -1) ? lgamma(v + 1.0) : 0;
+  T lcons = (2.0 + v) * log_half_z;
+  T out;
+  if (v > -1) {
+    out = log_sum_exp(v * log_half_z - lgam, lcons - lgamma(v + 2));
+    lgam += log1p(v);
+  } else {
+    out = lcons;
+  }
+
+  double m = 2;
+  double lfac = 0;
+  T old_out;
+  do {
+    lfac += log(m);
+    lgam += log(v + m);
+    lcons += 2 * log_half_z;
+    old_out = out;
+    out = log_sum_exp(out, lcons - lfac - lgam); // underflows eventually
+    m++;
+  } while (out > old_out || out < old_out);
+  return out;
+}
+
+} // namespace CosmoTool
+
+#endif