Merge pull request #44752 from costrouc/costrouc/lammps-update

material science packages (init and update): lammps, python - ase, pymatgen-lammps, lammps-cython, dftfit

pkgs/development/python-modules/ase/default.nix

@@ -0,0 +1,36 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, numpy
+, scipy
+, matplotlib
+, flask
+, pillow
+, psycopg2
+}:
+
+buildPythonPackage rec {
+  version = "3.16.2";
+  pname = "ase";
+
+  src = fetchurl {
+     url = "https://gitlab.com/${pname}/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
+     sha256 = "171j3f4a261cfnqjq98px5fldxql65i3jgf60wc945xvh0mbc8ds";
+  };
+
+  propagatedBuildInputs = [ numpy scipy matplotlib flask pillow psycopg2 ];
+
+  checkPhase = ''
+    $out/bin/ase test
+  '';
+
+  # tests just hang most likely due to something with subprocesses and cli
+  doCheck = false;
+
+  meta = {
+    description = "Atomic Simulation Environment";
+    homepage = https://wiki.fysik.dtu.dk/ase/;
+    license = lib.licenses.lgpl21Plus;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/dftfit/default.nix

@@ -0,0 +1,47 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+, pymatgen
+, marshmallow
+, pyyaml
+, pygmo
+, pandas
+, scipy
+, numpy
+, scikitlearn
+, lammps-cython
+, pymatgen-lammps
+, pytestrunner
+, pytest
+, pytestcov
+, pytest-benchmark
+, isPy3k
+, openssh
+}:
+
+buildPythonPackage rec {
+  pname = "dftfit";
+  version = "0.4.11";
+  disabled = (!isPy3k);
+
+  src = fetchPypi {
+     inherit pname version;
+     sha256 = "c6e36a793f9f94746bb8a04fb8316404aeacfa918704de07b15e1b4b8b62242d";
+  };
+
+  buildInputs = [ pytestrunner ];
+  checkInputs = [ pytest pytestcov pytest-benchmark openssh ];
+  propagatedBuildInputs = [ pymatgen marshmallow pyyaml pygmo
+                            pandas scipy numpy scikitlearn
+                            lammps-cython pymatgen-lammps ];
+
+  # tests require git lfs download. and is quite large so skip tests
+  doCheck = false;
+
+  meta = {
+    description = "Ab-Initio Molecular Dynamics Potential Development";
+    homepage = https://gitlab.com/costrouc/dftfit;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/docutils/default.nix

@@ -0,0 +1,35 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, isPy3k
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "docutils";
+  version = "0.14";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/docutils/${pname}.tar.gz";
+    sha256 = "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji";
+  };
+
+  checkPhase = if isPy3k then ''
+    ${python.interpreter} test3/alltests.py
+  '' else ''
+    ${python.interpreter} test/alltests.py
+  '';
+
+  # Create symlinks lacking a ".py" suffix, many programs depend on these names
+  postFixup = ''
+    (cd $out/bin && for f in *.py; do
+      ln -s $f $(echo $f | sed -e 's/\.py$//')
+    done)
+  '';
+
+  meta = {
+    description = "Docutils -- Python Documentation Utilities";
+    homepage = http://docutils.sourceforge.net/;
+    maintainers = with lib.maintainers; [ garbas AndersonTorres ];
+  };
+}

pkgs/development/python-modules/lammps-cython/default.nix

@@ -0,0 +1,53 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, lammps-mpi
+, mpi
+, mpi4py
+, numpy
+, cython
+, pymatgen
+, ase
+, pytestrunner
+, pytest
+, pytestcov
+, isPy3k
+, openssh
+}:
+
+buildPythonPackage rec {
+  pname = "lammps-cython";
+  version = "0.5.7";
+  disabled = (!isPy3k);
+
+  src = fetchurl {
+     url = "https://gitlab.com/costrouc/${pname}/-/archive/v${version}/${pname}-v${version}.tar.gz";
+     sha256 = "1wj9scmjdl00af13b5ihfccrjpikrdgkzd88ialam1nkxvxi42bl";
+  };
+
+  buildInputs = [ cython pytestrunner ];
+  checkInputs = [ pytest pytestcov openssh ];
+  propagatedBuildInputs = [ mpi4py pymatgen ase numpy ];
+
+  preBuild = ''
+    echo "Creating lammps.cfg file..."
+    cat << EOF > lammps.cfg
+    [lammps]
+    lammps_include_dir = ${lammps-mpi}/include
+    lammps_library_dir = ${lammps-mpi}/lib
+    lammps_library = lammps_mpi
+
+    [mpi]
+    mpi_include_dir = ${mpi}/include
+    mpi_library_dir = ${mpi}/lib
+    mpi_library     = mpi
+    EOF
+  '';
+
+  meta = {
+    description = "Pythonic Wrapper to LAMMPS using cython";
+    homepage = https://gitlab.com/costrouc/lammps-cython;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/pathlib/default.nix

@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, python
+, pythonAtLeast
+}:
+
+buildPythonPackage rec {
+  pname = "pathlib";
+  version = "1.0.1";
+  disabled = pythonAtLeast "3.4"; # Was added to std library in Python 3.4
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "17zajiw4mjbkkv6ahp3xf025qglkj0805m9s41c45zryzj6p2h39";
+  };
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover
+  '';
+
+  meta = {
+    description = "Object-oriented filesystem paths";
+    homepage = https://pathlib.readthedocs.org/;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/py-cpuinfo/default.nix

@@ -0,0 +1,23 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+}:
+
+buildPythonPackage rec {
+  pname = "py-cpuinfo";
+  version = "4.0.0";
+
+  src = fetchFromGitHub {
+     owner = "workhorsy";
+     repo = pname;
+     rev = "v${version}";
+     sha256 = "1pp561lj80jnvr2038nrzhmks2akxsbdqxvfrqa6n340x81981lm";
+  };
+
+  meta = {
+    description = "Get CPU info with pure Python 2 & 3";
+    homepage = https://github.com/workhorsy/py-cpuinfo;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/pygmo/default.nix

@@ -0,0 +1,48 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+, cmake
+, eigen
+, nlopt
+, ipopt
+, boost
+, pagmo2
+, numpy
+, cloudpickle
+, ipyparallel
+, numba
+}:
+
+buildPythonPackage rec {
+  pname = "pygmo";
+  version = "2.8";
+
+  src = fetchFromGitHub {
+     owner = "esa";
+     repo = "pagmo2";
+     rev = "v${version}";
+     sha256 = "1xwxamcn3fkwr62jn6bkanrwy0cvsksf75hfwx4fvl56awnbz41z";
+  };
+
+  buildInputs = [ cmake eigen nlopt ipopt boost pagmo2 ];
+  propagatedBuildInputs = [ numpy cloudpickle ipyparallel numba ];
+
+  preBuild = ''
+    cp -v -r $src/* .
+    cmake -DCMAKE_INSTALL_PREFIX=$out -DPAGMO_BUILD_TESTS=no -DCMAKE_SYSTEM_NAME=Linux -DPagmo_DIR=${pagmo2} -DPAGMO_BUILD_PYGMO=yes -DPAGMO_BUILD_PAGMO=no -DPAGMO_WITH_EIGEN3=yes -DPAGMO_WITH_NLOPT=yes -DNLOPT_LIBRARY=${nlopt}/lib/libnlopt_cxx.so -DPAGMO_WITH_IPOPT=yes -DIPOPT=${ipopt}
+
+    make install
+    mv $out/lib/python*/site-packages/pygmo wheel
+    cd wheel
+  '';
+
+  # dont do tests
+  doCheck = false;
+
+  meta = {
+    description = "Parallel optimisation for Python";
+    homepage = https://esa.github.io/pagmo2/;
+    license = lib.licenses.gpl3Plus;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/pymatgen-lammps/default.nix

@@ -0,0 +1,31 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, pymatgen
+, lammps
+, pytestrunner
+, pytest
+, isPy3k
+}:
+
+buildPythonPackage rec {
+  pname = "pymatgen-lammps";
+  version = "0.4.5";
+  disabled = (!isPy3k);
+
+  src = fetchurl {
+     url = "https://gitlab.com/costrouc/${pname}/-/archive/v${version}/${pname}-v${version}.tar.gz";
+     sha256 = "0shldl8is3195jmji7dr3zsh1bzxlahaqrmpr28niks7nnfj80fx";
+  };
+
+  buildInputs = [ pytestrunner ];
+  checkInputs = [ pytest ];
+  propagatedBuildInputs = [ pymatgen ];
+
+  meta = {
+    description = "A LAMMPS wrapper using pymatgen";
+    homepage = https://gitlab.com/costrouc/pymatgen-lammps;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/pytest-benchmark/default.nix

@@ -0,0 +1,31 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestrunner
+, pytest
+, py-cpuinfo
+, pythonOlder
+, pathlib
+, statistics
+}:
+
+buildPythonPackage rec {
+  pname = "pytest-benchmark";
+  version = "3.1.1";
+
+  src = fetchFromGitHub {
+    owner = "ionelmc";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1ch079dlc6c9ag74dh4dg6plkmh0h8kn78ari3fgadc75bald71m";
+  };
+
+  propagatedBuildInputs = [ pytest py-cpuinfo ] ++ lib.optional (pythonOlder "3.4") [ pathlib statistics ];
+
+  meta = {
+    description = "Py.test fixture for benchmarking code";
+    homepage = https://github.com/ionelmc/pytest-benchmark;
+    license = lib.licenses.bsd2;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/statistics/default.nix

@@ -0,0 +1,27 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+, docutils
+}:
+
+buildPythonPackage rec {
+  pname = "statistics";
+  version = "1.0.3.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138";
+  };
+
+  propagatedBuildInputs = [ docutils ];
+
+  # statistics package does not have any tests
+  doCheck = false;
+
+  meta = {
+    description = "A Python 2.* port of 3.4 Statistics Module";
+    homepage = https://github.com/digitalemagine/py-statistics;
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}