diff --git a/flake.lock b/flake.lock index 30e3c58..f87026f 100644 --- a/flake.lock +++ b/flake.lock @@ -18,26 +18,139 @@ "type": "github" } }, + "flake-utils_2": { + "inputs": { + "systems": "systems_2" + }, + "locked": { + "lastModified": 1710146030, + "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "nix-github-actions": { + "inputs": { + "nixpkgs": [ + "poetry2nix", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1703863825, + "narHash": "sha256-rXwqjtwiGKJheXB43ybM8NwWB8rO2dSRrEqes0S7F5Y=", + "owner": "nix-community", + "repo": "nix-github-actions", + "rev": "5163432afc817cf8bd1f031418d1869e4c9d5547", + "type": "github" + }, + "original": { + "owner": "nix-community", + "repo": "nix-github-actions", + "type": "github" + } + }, "nixpkgs": { "locked": { - "lastModified": 1717786204, - "narHash": "sha256-4q0s6m0GUcN7q+Y2DqD27iLvbcd1G50T2lv08kKxkSI=", + "lastModified": 1717880976, + "narHash": "sha256-BRvSCsKtDUr83NEtbGfHLUOdDK0Cgbezj2PtcHnz+sQ=", "owner": "nixos", "repo": "nixpkgs", - "rev": "051f920625ab5aabe37c920346e3e69d7d34400e", + "rev": "4913a7c3d8b8d00cb9476a6bd730ff57777f740c", "type": "github" }, "original": { "owner": "nixos", - "ref": "nixos-unstable", + "ref": "nixos-23.11", "repo": "nixpkgs", "type": "github" } }, + "nixpkgs_2": { + "locked": { + "lastModified": 1717298511, + "narHash": "sha256-9sXuJn/nL+9ImeYtlspTvjt83z1wIgU+9AwfNbnq+tI=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "6634a0509e9e81e980b129435fbbec518ab246d0", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixos-unstable-small", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs_3": { + "locked": { + "lastModified": 1717893485, + "narHash": "sha256-WMU6ZRZrBgEUDIF0siu2aIyVAXcxfElSwzZtS/mSpN4=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "3bcedce9f4de37570242faf16e1e143583407eab", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixpkgs-unstable", + "repo": "nixpkgs", + "type": "github" + } + }, + "poetry2nix": { + "inputs": { + "flake-utils": "flake-utils_2", + "nix-github-actions": "nix-github-actions", + "nixpkgs": "nixpkgs_2", + "systems": "systems_3", + "treefmt-nix": "treefmt-nix" + }, + "locked": { + "lastModified": 1717965289, + "narHash": "sha256-62VsS1MvwcsyYWnxxOD9rX5yqDUvMXH7qE3Kj8HECYE=", + "owner": "nix-community", + "repo": "poetry2nix", + "rev": "304f8235fb0729fd48567af34fcd1b58d18f9b95", + "type": "github" + }, + "original": { + "owner": "nix-community", + "repo": "poetry2nix", + "type": "github" + } + }, + "qchem": { + "inputs": { + "nixpkgs": "nixpkgs_3" + }, + "locked": { + "lastModified": 1718043075, + "narHash": "sha256-63gzno3k7SzCoXQjv7PGwU0mR6tLFTl1WTZwhfGu+ZQ=", + "owner": "Nix-QChem", + "repo": "NixOS-QChem", + "rev": "9286ea81c45be7cfd251a4584190b6e744b4c314", + "type": "github" + }, + "original": { + "owner": "Nix-QChem", + "repo": "NixOS-QChem", + "type": "github" + } + }, "root": { "inputs": { "flake-utils": "flake-utils", - "nixpkgs": "nixpkgs" + "nixpkgs": "nixpkgs", + "poetry2nix": "poetry2nix", + "qchem": "qchem" } }, "systems": { @@ -54,6 +167,56 @@ "repo": "default", "type": "github" } + }, + "systems_2": { + "locked": { + "lastModified": 1681028828, + "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=", + "owner": "nix-systems", + "repo": "default", + "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", + "type": "github" + }, + "original": { + "owner": "nix-systems", + "repo": "default", + "type": "github" + } + }, + "systems_3": { + "locked": { + "lastModified": 1681028828, + "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=", + "owner": "nix-systems", + "repo": "default", + "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", + "type": "github" + }, + "original": { + "id": "systems", + "type": "indirect" + } + }, + "treefmt-nix": { + "inputs": { + "nixpkgs": [ + "poetry2nix", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1717278143, + "narHash": "sha256-u10aDdYrpiGOLoxzY/mJ9llST9yO8Q7K/UlROoNxzDw=", + "owner": "numtide", + "repo": "treefmt-nix", + "rev": "3eb96ca1ae9edf792a8e0963cc92fddfa5a87706", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "treefmt-nix", + "type": "github" + } } }, "root": "root", diff --git a/flake.nix b/flake.nix index c1a60ce..2be152a 100644 --- a/flake.nix +++ b/flake.nix @@ -2,28 +2,77 @@ description = "SAPT energy calculator built using MDAnalysis and Psi4 "; inputs = { - nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable"; + nixpkgs.url = "github:nixos/nixpkgs/nixos-23.11"; flake-utils.url = "github:numtide/flake-utils"; + poetry2nix.url = "github:nix-community/poetry2nix"; + qchem.url = "github:Nix-QChem/NixOS-QChem"; }; - outputs = { self, nixpkgs, flake-utils}: + outputs = { self, nixpkgs, flake-utils, poetry2nix, qchem }: flake-utils.lib.eachDefaultSystem (system: let lib = nixpkgs.lib; - pkgs = nixpkgs.legacyPackages.${system}; + pkgs = import nixpkgs { + system = system; + overlays = [ + qchem.overlays.qchem + poetry2nix.overlays.default + ]; + }; + + + cython = with pkgs.python3Packages; cython_3.overrideAttrs (oldAttrs: rec { + version = "3.0.10"; + src = fetchPypi { + pname = "Cython"; + inherit version; + hash = "sha256-3MlnOTMfuFTc9QP5RgdXbP6EiAZsYcpQ39VYNvEy3pk="; + }; + }); + + pypkgs-build-reqs = { + mdanalysis = [ "setuptools" ]; + mda-xdrlib = [ "setuptools" ]; + mmtf-python = [ "setuptools" ]; + mrcfile = [ "setuptools" ]; + scipy = [ "setuptools" "wheel" "pybind11" "pythran" ]; + }; + + p2n-overrides = pkgs.poetry2nix.defaultPoetryOverrides.extend (final: prev: + builtins.mapAttrs (package: build-reqs: + (builtins.getAttr package prev).overridePythonAttrs (old: { + buildInputs = (old.buildInputs or [ ]) ++ (builtins.map (pkg: if builtins.isString pkg then builtins.getAttr pkg prev else pkg) build-reqs); + }) + ) pypkgs-build-reqs + ); + unfuckScipy = final: prev: { + cython = cython; + cython_3 = cython; + scipy = prev.scipy.overridePythonAttrs (old: { + buildInputs = old.buildInputs ++(with final; [ cython setuptools wheel pythran pybind11 ]); + }); + }; + + devEnv = pkgs.poetry2nix.mkPoetryEnv { + projectDir = ./.; + extraPackages = (ps: [ pkgs.qchem.psi4 pkgs.qchem.openmm ]); + python = pkgs.python311.override { + packageOverrides = pfinal: pprev: { + cython = cython; + cython_3 = cython; + }; + }; + overrides = [p2n-overrides unfuckScipy ]; + }; # DON'T FORGET TO PUT YOUR PACKAGE NAME HERE, REMOVING `throw` packageName = "MD-SAPT"; in { - - devShells.default = pkgs.mkShell { - buildInputs = [ - pkgs.poetry - ]; - }; + test.cython = cython; + devShells.default = devEnv; }); } diff --git a/poetry.lock b/poetry.lock index f98e933..bd7c17a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. [[package]] name = "click" version = "8.1.7" description = "Composable command line interface toolkit" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -18,6 +19,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -29,6 +31,7 @@ files = [ name = "contourpy" version = "1.2.1" description = "Python library for calculating contours of 2D quadrilateral grids" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -92,6 +95,7 @@ test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"] name = "cycler" version = "0.12.1" description = "Composable style cycles" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -103,10 +107,79 @@ files = [ docs = ["ipython", 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"1.0.2" description = "Reading and writing of data on regular grids in Python" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -199,6 +274,7 @@ scipy = "*" name = "importlib-resources" version = "6.4.0" description = "Read resources from Python packages" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -217,6 +293,7 @@ testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "p name = "joblib" version = "1.4.2" description = "Lightweight pipelining with Python functions" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -228,6 +305,7 @@ files = [ name = "kiwisolver" version = "1.4.5" description = "A fast implementation of the Cassowary constraint solver" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -341,6 +419,7 @@ files = [ name = "matplotlib" version = "3.9.0" description = "Python plotting package" +category = "main" optional = false python-versions = 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files = [ @@ -814,6 +906,7 @@ files = [ name = "threadpoolctl" version = "3.5.0" description = "threadpoolctl" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -825,6 +918,7 @@ files = [ name = "tqdm" version = "4.66.4" description = "Fast, Extensible Progress Meter" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -845,6 +939,7 @@ telegram = ["requests"] name = "zipp" version = "3.19.2" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -859,4 +954,4 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "35e27449f77df4aa02948651e81553ce382902239391da76bc88ce79d36e6184" +content-hash = "61b102d5232685da21c0df667e71bc8aa890f0a6e948cc73a89f5dd06420818c" diff --git a/pyproject.toml b/pyproject.toml index 2c9fadb..526c4b3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,6 +8,7 @@ readme = "README.md" [tool.poetry.dependencies] python = "^3.9" +cython = "^3.0.8" mdanalysis = "^2.7" click = "^8.1.7" rdkit = "^2023.9.6"