project structure and license+setup.py

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Valentin Boettcher
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+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 AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

flake.nix

@@ -1,31 +1,85 @@
 {
-  description = "Calculating open system bath energy changes with HOPS and analytically. ";
+  description = "Calculating open system bath energy changes with HOPS and analytically.";
 
   inputs = {
     nixpkgs.url = "nixpkgs/nixos-unstable";
     mach-nix.url = "github:DavHau/mach-nix";
+    flake-utils.url = "github:numtide/flake-utils";
   };
 
    outputs = { self, nixpkgs, flake-utils, mach-nix }:
-    flake-utils.lib.eachDefaultSystem (system:
      let
        python = "python39";
-        pkgs = nixpkgs.legacyPackages.${system};
+       pypiDataRev = "master";
-
+       pypiDataSha256 = "041rpjrwwa43hap167jy8blnxvpvbfil0ail4y4mar1q5f0q57xx";
-        mach-nix-wrapper = import mach-nix { inherit pkgs python; };
+       devShell = pkgs:
-        requirements = builtins.readFile ./requirements.txt;
+         pkgs.mkShell {
-        pythonBuild = mach-nix-wrapper.mkPython { inherit requirements; };
-      in {
-        devShell = pkgs.mkShell {
            buildInputs = [
-            # dev packages
              (pkgs.${python}.withPackages
-              (ps: with ps; [ black mypy sphinx-autodoc-typehints sphinx pydata-sphinx-theme  ])) # <--- change here
+               (ps: with ps; [ black mypy ]))
              pkgs.nodePackages.pyright
-
-            # app packages
-            pythonBuild
            ];
          };
+
+     in flake-utils.lib.eachDefaultSystem (system:
+       let
+         pkgs = nixpkgs.legacyPackages.${system};
+         mach-nix-wrapper = import mach-nix { inherit pkgs python pypiDataRev pypiDataSha256; };
+
+         fcSpline = (mach-nix-wrapper.buildPythonPackage
+           {src = builtins.fetchTarball {
+              url = "https://github.com/cimatosa/fcSpline/archive/4312b2c63d52711bff1bfe282d92f98a3e5073fb.tar.gz";
+              sha256 = "0l38q5avcbiyqlmmhznw9sg02y54fia6r7x2f9w6h3kqf2xh05yc";
+            };
+            pname="fcSpline";
+            version="0.1";
+            requirements=''
+             numpy
+             cython
+             setuptools
+             scipy
+           '';
+           });
+
+         stocproc = (mach-nix-wrapper.buildPythonPackage
+           {src = builtins.fetchTarball {
+              url = "https://github.com/vale981/stocproc/archive/c81eead1b86d8da0caa5ec013b5fb65e9d3c3b79.tar.gz";
+              sha256 = "00fvfmdcpkm9lp2zn8kzzn6msq7cypqhf87ihrf63ci5z4hg2jpl";
+            };
+            pname="stocproc";
+            version = "1.0.1";
+            requirements = ''
+             numpy
+             cython
+             setuptools
+             mpmath
+             scipy
+             '';
+           });
+
+         requirements = builtins.readFile ./requirements.txt;
+
+         pythonShell = mach-nix-wrapper.mkPythonShell {
+           requirements = requirements + ''
+           sphinx
+           pydata-sphinx-theme
+           sphinx-autodoc-typehints
+           data-science-types
+           '';
+           packagesExtra = [fcSpline stocproc];
+           _.stocproc.buildInputs.add = [fcSpline];
+         };
+
+         pythonPackage = mach-nix-wrapper.buildPythonPackage ./setup.py;
+
+         mergeEnvs = envs:
+           pkgs.mkShell (builtins.foldl' (a: v: {
+             buildInputs = a.buildInputs ++ v.buildInputs;
+             nativeBuildInputs = a.nativeBuildInputs ++ v.nativeBuildInputs;
+           }) (pkgs.mkShell { }) envs);
+
+       in {
+         devShell = mergeEnvs [ (devShell pkgs) pythonShell ];
+         defaultPackage = pythonPackage;
        });
 }

hopsflow/setup.py

@@ -0,0 +1,11 @@
+from distutils.core import setup
+
+setup(
+    name="Distutils",
+    version="1.0",
+    description="Python Distribution Utilities",
+    author="Greg Ward",
+    author_email="gward@python.net",
+    url="https://www.python.org/sigs/distutils-sig/",
+    packages=["distutils", "distutils.command"],
+)

requirements.txt

@@ -1,6 +1,5 @@
 numpy >= 1.20
-data-science-types
 scipy >= 1.6
 h5py
-sqlitedict
 tqdm
+lmfit

setup.cfg

@@ -1,15 +0,0 @@
-[flake8]
-ignore = E501
-max-line-length = 120
-
-[mypy]
-exclude = docs
-
-[mypy-stocproc.*]
-ignore_missing_imports = True
-
-[mypy-scipy.*]
-ignore_missing_imports = True
-
-[mypy-lmfit.*]
-ignore_missing_imports = True

setup.py

@@ -0,0 +1,12 @@
+from distutils.core import setup
+
+setup(
+    name="hopsflow",
+    version="1.0",
+    description="Calculating open system bath energy changes with HOPS and analytically.",
+    author="Valentin Boettcher",
+    author_email="hiro@protagon.space",
+    url="https://github.com/vale981/hopsflow",
+    packages=["hopsflow"],
+    install_requires=["numpy >= 1.20", "scipy >= 1.6", "h5py", "tqdm", "lmfit"],
+)