toolchain: migrate from requirements.txt to poetry

poetry: add deps from requirements.txt
flake: import poetry with poetry2nix
doc: update installation section

README.md

@@ -2,18 +2,24 @@
 
 A time domain simulation for WRPLL
 
-## Installing dependencies
+## Installation
+
+### Poetry:
+```bash
+poetry install --no-root
+poetry run jupyter lab
+```
+
+### Poetry shell:
+```bash
+poetry install --no-root
+poetry shell
+```
 
 ### Nix:
 ```bash
 nix develop
 ```
-### Others:
-```bash
-python -m venv .venv
-source .venv/bin/activate
-(venv) pip install -r requirements.txt
-```
 
 ## Quick start
 - Three notebook examples are included 

flake.lock

@@ -1,5 +1,44 @@
 {
   "nodes": {
+    "flake-utils": {
+      "inputs": {
+        "systems": "systems"
+      },
+      "locked": {
+        "lastModified": 1694529238,
+        "narHash": "sha256-zsNZZGTGnMOf9YpHKJqMSsa0dXbfmxeoJ7xHlrt+xmY=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "ff7b65b44d01cf9ba6a71320833626af21126384",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nix-github-actions": {
+      "inputs": {
+        "nixpkgs": [
+          "poetry2nix",
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1698974481,
+        "narHash": "sha256-yPncV9Ohdz1zPZxYHQf47S8S0VrnhV7nNhCawY46hDA=",
+        "owner": "nix-community",
+        "repo": "nix-github-actions",
+        "rev": "4bb5e752616262457bc7ca5882192a564c0472d2",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "nix-github-actions",
+        "type": "github"
+      }
+    },
     "nixpkgs": {
       "locked": {
         "lastModified": 1702233072,
@@ -16,9 +55,84 @@
         "type": "github"
       }
     },
+    "poetry2nix": {
+      "inputs": {
+        "flake-utils": "flake-utils",
+        "nix-github-actions": "nix-github-actions",
+        "nixpkgs": [
+          "nixpkgs"
+        ],
+        "systems": "systems_2",
+        "treefmt-nix": "treefmt-nix"
+      },
+      "locked": {
+        "lastModified": 1702365004,
+        "narHash": "sha256-IRFvmyP1uk1hchRVxaXTqu6YoZCvMM/NVtUf2hD2Tag=",
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "c12ac880114d52a3cad5fa02b00f2e2090e89982",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "type": "github"
+      }
+    },
     "root": {
       "inputs": {
-        "nixpkgs": "nixpkgs"
+        "nixpkgs": "nixpkgs",
+        "poetry2nix": "poetry2nix"
+      }
+    },
+    "systems": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
+    },
+    "systems_2": {
+      "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": 1699786194,
+        "narHash": "sha256-3h3EH1FXQkIeAuzaWB+nK0XK54uSD46pp+dMD3gAcB4=",
+        "owner": "numtide",
+        "repo": "treefmt-nix",
+        "rev": "e82f32aa7f06bbbd56d7b12186d555223dc399d1",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "treefmt-nix",
+        "type": "github"
       }
     }
   },

flake.nix

@@ -1,37 +1,50 @@
 {
-  inputs = { nixpkgs.url = "github:nixos/nixpkgs/nixos-23.11"; };
+  inputs = {
-  outputs = { nixpkgs, ... }:
+    nixpkgs.url = "github:nixos/nixpkgs/nixos-23.11";
-
+    poetry2nix = {
+      url = "github:nix-community/poetry2nix";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+  };
+  outputs = { nixpkgs, poetry2nix, ... }:
     let
 
       pkgs = import nixpkgs { system = "x86_64-linux"; };
+      poetry2nixlib = (poetry2nix.lib.mkPoetry2Nix { inherit pkgs; });
 
-    in
+      poetryEnv = poetry2nixlib.mkPoetryEnv {
-    rec {
+        python = pkgs.python3;
+        projectDir = ./.;
+        pyproject = ./pyproject.toml;
+        poetrylock = ./poetry.lock;
+        overrides = poetry2nixlib.overrides.withDefaults (self: super: {
+          trace-updater = super.trace-updater.overridePythonAttrs (
+            # ModuleNotFoundError: No module named 'setuptools'
+            old: {
+              buildInputs = (old.buildInputs or [ ]) ++ [ super.setuptools ];
+            });
+          tsdownsample = super.tsdownsample.override {
+            # for bypassing building with maturin
+            preferWheel = true;
+          };
+          plotly-resampler = super.plotly-resampler.overridePythonAttrs (
+            # ModuleNotFoundError: No module named 'poetry'
+            old: {
+              buildInputs = (old.buildInputs or [ ]) ++ [ super.poetry-core ];
+            });
+          scipy = super.scipy.override {
+            # fail to build
+            preferWheel = true;
+          };
+        });
+      };
+
+    in rec {
       formatter.x86_64-linux = nixpkgs.legacyPackages.x86_64-linux.nixfmt;
       devShell.x86_64-linux = pkgs.mkShell {
         name = "WRPLL-sim";
         venvDir = "./.venv";
-        buildInputs = with pkgs; [
+        buildInputs = with pkgs; [ poetryEnv poetry nixpkgs-fmt ];
-          nixpkgs-fmt
-          python3Packages.python
-          python3Packages.numba
-          python3Packages.numpy
-          python3Packages.notebook # use jupyter notebook without missing libstdc++.so.6
-          python3Packages.venvShellHook
-
-        ];
-
-        # Only run once when venv is created
-        postVenvCreation = ''
-          unset SOURCE_DATE_EPOCH
-          pip install -r requirements.txt
-        '';
-
-        postShellHook = ''
-          # allow pip to install wheels
-          unset SOURCE_DATE_EPOCH
-        '';
 
       };
     };

pyproject.toml

@@ -0,0 +1,23 @@
+[tool.poetry]
+name = "wrpll-simulation"
+version = "0.1.0"
+description = ""
+authors = ["morgan <mc@m-labs.hk>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.11"
+scipy = "^1.11.4"
+numpy = "^1.26.2"
+ipykernel = "^6.27.1"
+ipywidgets = "^8.1.1"
+jupyter = "^1.0.0"
+numba = "^0.58.1"
+pandas = "^2.1.4"
+plotly = "^5.18.0"
+plotly-resampler = "^0.9.1"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

requirements.txt

@@ -1,11 +0,0 @@
-scipy
-numpy
-ipykernel
-ipywidgets
-jupyter
-jupyterlab
-notebook
-numba
-pandas
-plotly
-plotly-resampler