From 9b4c88dc2884c470a56d7eda0a598ac4bd8df561 Mon Sep 17 00:00:00 2001 From: "R. Ryantm" Date: Sat, 27 Apr 2024 00:07:36 +0000 Subject: [PATCH 1/6] python311Packages.cdcs: 0.2.2 -> 0.2.3 --- pkgs/development/python-modules/cdcs/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/cdcs/default.nix b/pkgs/development/python-modules/cdcs/default.nix index 511a3975d97f..abd3d6f22fde 100644 --- a/pkgs/development/python-modules/cdcs/default.nix +++ b/pkgs/development/python-modules/cdcs/default.nix @@ -14,7 +14,7 @@ buildPythonPackage rec { pname = "cdcs"; - version = "0.2.2"; + version = "0.2.3"; format = "setuptools"; disabled = pythonOlder "3.6"; @@ -23,7 +23,7 @@ buildPythonPackage rec { owner = "usnistgov"; repo = "pycdcs"; rev = "refs/tags/v${version}"; - hash = "sha256-WiNjMMcpp5K+Re44ryB7LNzr2LnnYzLZ5b0iT7u1ZiA="; + hash = "sha256-HhAzULVWkKOWDJ6IZyBy0MYc/YGAFkSTLIgpdyvw1eI="; }; nativeBuildInputs = [ From a177409a58514552b7c700b41efc54591975c577 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Sat, 27 Apr 2024 14:30:03 +0200 Subject: [PATCH 2/6] python311Packages.cdcs: refactor --- pkgs/development/python-modules/cdcs/default.nix | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pkgs/development/python-modules/cdcs/default.nix b/pkgs/development/python-modules/cdcs/default.nix index abd3d6f22fde..9baf0bb566b0 100644 --- a/pkgs/development/python-modules/cdcs/default.nix +++ b/pkgs/development/python-modules/cdcs/default.nix @@ -15,9 +15,9 @@ buildPythonPackage rec { pname = "cdcs"; version = "0.2.3"; - format = "setuptools"; + pyproject = true; - disabled = pythonOlder "3.6"; + disabled = pythonOlder "3.8"; src = fetchFromGitHub { owner = "usnistgov"; @@ -26,11 +26,11 @@ buildPythonPackage rec { hash = "sha256-HhAzULVWkKOWDJ6IZyBy0MYc/YGAFkSTLIgpdyvw1eI="; }; - nativeBuildInputs = [ + build-system = [ setuptools ]; - propagatedBuildInputs = [ + dependencies = [ ipython numpy pandas From eba7be3db97313dd974b6fe259e482a7fe4e5317 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Sat, 27 Apr 2024 14:30:22 +0200 Subject: [PATCH 3/6] python311Packages.cdcs: format with nixfmt --- .../python-modules/cdcs/default.nix | 33 +++++++++---------- 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/pkgs/development/python-modules/cdcs/default.nix b/pkgs/development/python-modules/cdcs/default.nix index 9baf0bb566b0..38c643cd10a4 100644 --- a/pkgs/development/python-modules/cdcs/default.nix +++ b/pkgs/development/python-modules/cdcs/default.nix @@ -1,15 +1,16 @@ -{ lib -, buildPythonPackage -, fetchFromGitHub -, ipython -, numpy -, pandas -, pytestCheckHook -, pythonOlder -, requests -, responses -, setuptools -, tqdm +{ + lib, + buildPythonPackage, + fetchFromGitHub, + ipython, + numpy, + pandas, + pytestCheckHook, + pythonOlder, + requests, + responses, + setuptools, + tqdm, }: buildPythonPackage rec { @@ -26,9 +27,7 @@ buildPythonPackage rec { hash = "sha256-HhAzULVWkKOWDJ6IZyBy0MYc/YGAFkSTLIgpdyvw1eI="; }; - build-system = [ - setuptools - ]; + build-system = [ setuptools ]; dependencies = [ ipython @@ -43,9 +42,7 @@ buildPythonPackage rec { responses ]; - pythonImportsCheck = [ - "cdcs" - ]; + pythonImportsCheck = [ "cdcs" ]; meta = with lib; { description = "Python client for performing REST calls to configurable data curation system (CDCS) databases"; From 0760614080cedf70383eb82a2133f7d9b830eddf Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Sat, 27 Apr 2024 14:51:09 +0200 Subject: [PATCH 4/6] python312Packages.pymatgen: refactor --- .../python-modules/pymatgen/default.nix | 26 ++++++++++++------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/pkgs/development/python-modules/pymatgen/default.nix b/pkgs/development/python-modules/pymatgen/default.nix index cccf04f3a21a..0c19f32aa75a 100644 --- a/pkgs/development/python-modules/pymatgen/default.nix +++ b/pkgs/development/python-modules/pymatgen/default.nix @@ -1,27 +1,28 @@ { lib , stdenv -, buildPythonPackage -, fetchFromGitHub , ase +, buildPythonPackage , cython +, fetchFromGitHub , glibcLocales , joblib , matplotlib , monty , networkx -, numpy +, oldest-supported-numpy , palettable , pandas , plotly , pybtex , pydispatcher -, pytestCheckHook , pytest-xdist +, pytestCheckHook , pythonOlder , requests , ruamel-yaml , scipy , seekpath +, setuptools , spglib , sympy , tabulate @@ -31,27 +32,31 @@ buildPythonPackage rec { pname = "pymatgen"; version = "2024.2.23"; - format = "setuptools"; + pyproject = true; disabled = pythonOlder "3.8"; src = fetchFromGitHub { owner = "materialsproject"; repo = "pymatgen"; - rev= "v${version}"; + rev= "refs/tags/v${version}"; hash = "sha256-eswoup9ACj/PHVW3obcnZjD4tWemsmROZFtwGGigEYE="; }; + build-system = [ + setuptools + ]; + nativeBuildInputs = [ cython glibcLocales ]; - propagatedBuildInputs = [ + dependencies = [ matplotlib monty networkx - numpy + oldest-supported-numpy palettable pandas plotly @@ -70,6 +75,7 @@ buildPythonPackage rec { pytestCheckHook pytest-xdist ] ++ lib.flatten (builtins.attrValues passthru.optional-dependencies); + preCheck = '' # hide from tests mv pymatgen _pymatgen @@ -78,6 +84,7 @@ buildPythonPackage rec { # some tests cover the command-line scripts export PATH=$out/bin:$PATH ''; + disabledTests = [ # presumably won't work with our dir layouts "test_egg_sources_txt_is_complete" @@ -96,10 +103,11 @@ buildPythonPackage rec { ]; meta = with lib; { - broken = stdenv.isDarwin; # tests segfault. that's bad. description = "A robust materials analysis code that defines core object representations for structures and molecules"; homepage = "https://pymatgen.org/"; + changelog = "https://github.com/materialsproject/pymatgen/releases/tag/v${version}"; license = licenses.mit; maintainers = with maintainers; [ psyanticy ]; + broken = stdenv.isDarwin; # tests segfault. that's bad. }; } From 0d9c130d7546f39a85e279ec4a3eca824a61bfe2 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Sat, 27 Apr 2024 15:03:43 +0200 Subject: [PATCH 5/6] python312Packages.pymatgen: 2024.2.23 -> 2024.4.13 Diff: https://github.com/materialsproject/pymatgen/compare/refs/tags/v2024.2.23...v2024.4.13 Changelog: https://github.com/materialsproject/pymatgen/releases/tag/v2024.4.13 --- .../python-modules/pymatgen/default.nix | 23 ++++++++++++------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/pkgs/development/python-modules/pymatgen/default.nix b/pkgs/development/python-modules/pymatgen/default.nix index 0c19f32aa75a..f667752779cd 100644 --- a/pkgs/development/python-modules/pymatgen/default.nix +++ b/pkgs/development/python-modules/pymatgen/default.nix @@ -31,7 +31,7 @@ buildPythonPackage rec { pname = "pymatgen"; - version = "2024.2.23"; + version = "2024.4.13"; pyproject = true; disabled = pythonOlder "3.8"; @@ -40,7 +40,7 @@ buildPythonPackage rec { owner = "materialsproject"; repo = "pymatgen"; rev= "refs/tags/v${version}"; - hash = "sha256-eswoup9ACj/PHVW3obcnZjD4tWemsmROZFtwGGigEYE="; + hash = "sha256-vjasWQgwjtoM/6Y1HwK1otMFejRWEj+YBxaIYDDSeeo="; }; build-system = [ @@ -71,6 +71,12 @@ buildPythonPackage rec { uncertainties ]; + passthru.optional-dependencies = { + ase = [ ase ]; + joblib = [ joblib ]; + seekpath = [ seekpath ]; + }; + nativeCheckInputs = [ pytestCheckHook pytest-xdist @@ -90,14 +96,15 @@ buildPythonPackage rec { "test_egg_sources_txt_is_complete" # borderline precision failure "test_thermal_conductivity" + # AssertionError + "test_dict_functionality" + "test_mean_field" + "test_potcar_not_found" + "test_read_write_lobsterin" + "test_snl" + "test_unconverged" ]; - passthru.optional-dependencies = { - ase = [ ase ]; - joblib = [ joblib ]; - seekpath = [ seekpath ]; - }; - pythonImportsCheck = [ "pymatgen" ]; From 6ed2833404297a1f3bee0d48f5d0df92c79b84f0 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Sat, 27 Apr 2024 15:06:59 +0200 Subject: [PATCH 6/6] python312Packages.pymatgen: format with nixfmt --- .../python-modules/pymatgen/default.nix | 71 +++++++++---------- 1 file changed, 34 insertions(+), 37 deletions(-) diff --git a/pkgs/development/python-modules/pymatgen/default.nix b/pkgs/development/python-modules/pymatgen/default.nix index f667752779cd..59981da7e780 100644 --- a/pkgs/development/python-modules/pymatgen/default.nix +++ b/pkgs/development/python-modules/pymatgen/default.nix @@ -1,32 +1,33 @@ -{ lib -, stdenv -, ase -, buildPythonPackage -, cython -, fetchFromGitHub -, glibcLocales -, joblib -, matplotlib -, monty -, networkx -, oldest-supported-numpy -, palettable -, pandas -, plotly -, pybtex -, pydispatcher -, pytest-xdist -, pytestCheckHook -, pythonOlder -, requests -, ruamel-yaml -, scipy -, seekpath -, setuptools -, spglib -, sympy -, tabulate -, uncertainties +{ + lib, + stdenv, + ase, + buildPythonPackage, + cython, + fetchFromGitHub, + glibcLocales, + joblib, + matplotlib, + monty, + networkx, + oldest-supported-numpy, + palettable, + pandas, + plotly, + pybtex, + pydispatcher, + pytest-xdist, + pytestCheckHook, + pythonOlder, + requests, + ruamel-yaml, + scipy, + seekpath, + setuptools, + spglib, + sympy, + tabulate, + uncertainties, }: buildPythonPackage rec { @@ -39,13 +40,11 @@ buildPythonPackage rec { src = fetchFromGitHub { owner = "materialsproject"; repo = "pymatgen"; - rev= "refs/tags/v${version}"; + rev = "refs/tags/v${version}"; hash = "sha256-vjasWQgwjtoM/6Y1HwK1otMFejRWEj+YBxaIYDDSeeo="; }; - build-system = [ - setuptools - ]; + build-system = [ setuptools ]; nativeBuildInputs = [ cython @@ -105,9 +104,7 @@ buildPythonPackage rec { "test_unconverged" ]; - pythonImportsCheck = [ - "pymatgen" - ]; + pythonImportsCheck = [ "pymatgen" ]; meta = with lib; { description = "A robust materials analysis code that defines core object representations for structures and molecules"; @@ -115,6 +112,6 @@ buildPythonPackage rec { changelog = "https://github.com/materialsproject/pymatgen/releases/tag/v${version}"; license = licenses.mit; maintainers = with maintainers; [ psyanticy ]; - broken = stdenv.isDarwin; # tests segfault. that's bad. + broken = stdenv.isDarwin; # tests segfault. that's bad. }; }