endoreg-db 0.4.6__tar.gz → 0.5.0__tar.gz

endoreg_db-0.5.0/.envrc

@@ -0,0 +1 @@
+use flake

endoreg_db-0.5.0/.gitignore

@@ -0,0 +1,170 @@
+result
+result/
+*result
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+_build
+.direnv
+
+###### Do not Remove ######
+# Protects temporary files from being comitted
+endoreg_client_manager/data/*
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

endoreg_db-0.5.0/PKG-INFO

@@ -0,0 +1,25 @@
+Metadata-Version: 2.3
+Name: endoreg-db
+Version: 0.5.0
+Summary: EndoReg Db Django App
+Requires-Python: >=3.11
+Requires-Dist: django-bootstrap5>=24.3
+Requires-Dist: django>=5.1.3
+Requires-Dist: djangorestframework>=3.15.2
+Requires-Dist: ffmpeg-python>=0.2.0
+Requires-Dist: opencv-python>=4.10.0.84
+Requires-Dist: pillow>=11.0.0
+Requires-Dist: pytesseract>=0.3.13
+Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: scipy>=1.14.1
+Requires-Dist: tqdm>=4.67.0
+Description-Content-Type: text/markdown
+
+# endoreg-db
+endoreg-db
+
+
+## Poetry add pypi token
+poetry config pypi-token.pypi your-api-token
+
+

endoreg_db-0.5.0/_flake.nix

@@ -0,0 +1,130 @@
+{
+  description = "Flake for the EndoReg Db Django App";
+
+  nixConfig = {
+    substituters = [
+        "https://cache.nixos.org"
+        "https://cuda-maintainers.cachix.org"
+      ];
+    trusted-public-keys = [
+        "cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY="
+        "cuda-maintainers.cachix.org-1:0dq3bujKpuEPMCX6U4WylrUDZ9JyUG0VpVZa7CNfq5E="
+      ];
+    extra-substituters = "https://cache.nixos.org https://nix-community.cachix.org https://cuda-maintainers.cachix.org";
+    extra-trusted-public-keys = "cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY= nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs= cuda-maintainers.cachix.org-1:0dq3bujKpuEPMCX6U4WylrUDZ9JyUG0VpVZa7CNfq5E=";
+  };
+
+  inputs = {
+    poetry2nix.url = "github:nix-community/poetry2nix";
+    poetry2nix.inputs.nixpkgs.follows = "nixpkgs";
+
+    # agl-report-reader = {
+    #   url = "github:wg-lux/agl-report-reader";
+    #   inputs.nixpkgs.follows = "nixpkgs";
+    # };
+
+    cachix = {
+      url = "github:cachix/cachix";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+  };
+
+  outputs = { nixpkgs, poetry2nix, ... } @ inputs: 
+    let
+      system = "x86_64-linux";
+      self = inputs.self;
+      version = "0.1.${pkgs.lib.substring 0 8 inputs.self.lastModifiedDate}.${inputs.self.shortRev or "dirty"}";
+      python-version = "311";
+      cachix = inputs.cachix;
+
+      nvidiaCache = cachix.lib.mkCachixCache {
+        inherit (pkgs) lib;
+        name = "nvidia";
+        publicKey = "nvidia.cachix.org-1:dSyZxI8geDCJrwgvBfPH3zHMC+PO6y/BT7O6zLBOv0w=";
+        secretKey = null;  # not needed for pulling from the cache
+      };
+    
+      pkgs = import nixpkgs {
+        inherit system;
+        config = {
+          allowUnfree = true;
+        };
+      };
+
+      lib = pkgs.lib;
+
+      pypkgs-build-requirements = {
+        gender-guesser = [ "setuptools" ];
+        conllu = [ "setuptools" ];
+        janome = [ "setuptools" ];
+        pptree = [ "setuptools" ];
+        wikipedia-api = [ "setuptools" ];
+        django-flat-theme = [ "setuptools" ];
+        django-flat-responsive = [ "setuptools" ];
+      };
+
+      poetry2nix = inputs.poetry2nix.lib.mkPoetry2Nix { inherit pkgs;};
+
+      p2n-overrides = poetry2nix.defaultPoetryOverrides.extend (final: prev:
+        builtins.mapAttrs (package: build-requirements:
+          (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-requirements
+            );
+          })
+        ) pypkgs-build-requirements
+      );
+
+      poetryApp = poetry2nix.mkPoetryApplication {
+        projectDir = ./.;
+        src = lib.cleanSource ./.;
+        python = pkgs."python${python-version}";
+        overrides = p2n-overrides;
+        preferWheels = true; # some packages, e.g. transformers break if false
+
+        # Makes Package available to other packages which depend on this one (e.g. agl-monitor flake also imports functions from agl-report reader)
+        propagatedBuildInputs =  with pkgs."python${python-version}Packages"; [
+          # inputs.agl-report-reader.packages.x86_64-linux.poetryApp
+        ];
+        nativeBuildInputs = with pkgs."python${python-version}Packages"; [
+          pip
+          setuptools
+          # inputs.agl-report-reader.packages.x86_64-linux.poetryApp
+        ];
+      };
+
+      poetryAppDev = poetry2nix.mkPoetryEditablePackage {
+        projectDir = ./.;
+        python = pkgs."python${python-version}";
+        # python3 = python39;
+        editablePackageSources = {
+          endoreg-db = lib.cleanSource ./.;
+        };
+      };       
+      
+  in
+  {
+
+    packages.x86_64-linux.poetryAppDev = poetryAppDev;
+    packages.x86_64-linux.poetryApp = poetryApp;
+    packages.x86_64-linux.default = poetryApp;
+
+    apps.x86_64-linux.default = {
+      type = "app";
+      # program = "${poetryApp}/bin/django-server";
+    };
+
+    devShells.x86_64-linux.default = pkgs.mkShell {
+      inputsFrom = [ self.packages.x86_64-linux.poetryApp ];
+      packages = [ pkgs.poetry ];
+      shellHook = ''
+      '';
+    };
+
+  };
+}
+
+
+

endoreg_db-0.5.0/depreceated_pip-shell.nix

@@ -0,0 +1,12 @@
+# https://nixos.wiki/wiki/Python
+
+{ pkgs ? import <nixpkgs> {} }:
+(pkgs.buildFHSUserEnv {
+name = "pipzone";
+targetPkgs = pkgs: (with pkgs; [
+    python311
+    python311Packages.pip
+    python311Packages.virtualenv
+]);
+runScript = "bash";
+}).env

endoreg_db-0.5.0/flake.lock

@@ -0,0 +1,72 @@
+{
+  "nodes": {
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1731139594,
+        "narHash": "sha256-IigrKK3vYRpUu+HEjPL/phrfh7Ox881er1UEsZvw9Q4=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "76612b17c0ce71689921ca12d9ffdc9c23ce40b2",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "pyproject-nix": {
+      "inputs": {
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1731223003,
+        "narHash": "sha256-hFf8/IeZKPUubMC452Mm+JiAEnvcw/a4Cvn2bcpeJqs=",
+        "owner": "nix-community",
+        "repo": "pyproject.nix",
+        "rev": "359dd9cd562730bbd31ab164832aae4dacd9c302",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "pyproject.nix",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "nixpkgs": "nixpkgs",
+        "pyproject-nix": "pyproject-nix",
+        "uv2nix": "uv2nix"
+      }
+    },
+    "uv2nix": {
+      "inputs": {
+        "nixpkgs": [
+          "nixpkgs"
+        ],
+        "pyproject-nix": [
+          "pyproject-nix"
+        ]
+      },
+      "locked": {
+        "lastModified": 1731455524,
+        "narHash": "sha256-6uAgsZC5CChUtbLb9+MnNxhwL8uITbEh5zhPtQC3u8E=",
+        "owner": "adisbladis",
+        "repo": "uv2nix",
+        "rev": "e68500c8353abaab5bf2c789105eebd9e435fe76",
+        "type": "github"
+      },
+      "original": {
+        "owner": "adisbladis",
+        "repo": "uv2nix",
+        "type": "github"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

endoreg_db-0.5.0/flake.nix

@@ -0,0 +1,181 @@
+{
+  description = "Hello world flake using uv2nix";
+
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+
+    pyproject-nix = {
+      url = "github:nix-community/pyproject.nix";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+
+    uv2nix = {
+      url = "github:adisbladis/uv2nix";
+      inputs.pyproject-nix.follows = "pyproject-nix";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+  };
+
+  # Note that uv2nix is _not_ using Nixpkgs buildPythonPackage.
+  # It's using https://nix-community.github.io/pyproject.nix/build.html
+
+  outputs =
+    {
+      self,
+      nixpkgs,
+      uv2nix,
+      pyproject-nix,
+      ...
+    }:
+    let
+      inherit (nixpkgs) lib;
+      forAllSystems = lib.genAttrs lib.systems.flakeExposed;
+
+      # Load a uv workspace from a workspace root.
+      # Uv2nix treats all uv projects as workspace projects.
+      # https://adisbladis.github.io/uv2nix/lib/workspace.html
+      workspace = uv2nix.lib.workspace.loadWorkspace { workspaceRoot = ./.; };
+
+      # Create package overlay from workspace.
+      overlay = workspace.mkPyprojectOverlay {
+        sourcePreference = "wheel"; # or sourcePreference = "sdist";
+      };
+
+      editableOverlay = workspace.mkEditablePyprojectOverlay {
+        root = "$REPO_ROOT";
+      };
+
+      # Python sets grouped per system
+      pythonSets = forAllSystems (
+        system:
+        let
+          pkgs = nixpkgs.legacyPackages.${system};
+          inherit (pkgs) stdenv;
+
+          # Base Python package set from pyproject.nix
+          baseSet = pkgs.callPackage pyproject-nix.build.packages {
+            python = pkgs.python312;
+          };
+
+          # An overlay of build fixups & test additions
+          pyprojectOverrides = final: prev: {
+
+            endoreg-db = prev.endoreg-db.overrideAttrs (old: {
+
+              # Add tests to passthru.tests
+              #
+              # These attribute are used in Flake checks.
+              passthru = old.passthru // {
+                tests =
+                  (old.tests or { })
+                  // {
+
+                    # Run mypy checks
+                    mypy =
+                      let
+                        venv = final.mkVirtualEnv "endoreg-db-typing-env" {
+                          endoreg-db = [ "typing" ];
+                        };
+                      in
+                      stdenv.mkDerivation {
+                        name = "${final.endoreg-db.name}-mypy";
+                        inherit (final.endoreg-db) src;
+                        nativeBuildInputs = [
+                          venv
+                        ];
+                        dontConfigure = true;
+                        dontInstall = true;
+                        buildPhase = ''
+                          mkdir $out
+                          mypy --strict . --junit-xml $out/junit.xml
+                        '';
+                      };
+
+                    # Run pytest with coverage reports installed into build output
+                    pytest =
+                      let
+                        venv = final.mkVirtualEnv "endoreg-db-pytest-env" {
+                          endoreg-db = [ "test" ];
+                        };
+                      in
+                      stdenv.mkDerivation {
+                        name = "${final.endoreg-db.name}-pytest";
+                        inherit (final.endoreg-db) src;
+                        nativeBuildInputs = [
+                          venv
+                        ];
+
+                        dontConfigure = true;
+
+                        buildPhase = ''
+                          runHook preBuild
+                          pytest --cov tests --cov-report html tests
+                          runHook postBuild
+                        '';
+
+                        installPhase = ''
+                          runHook preInstall
+                          mv htmlcov $out
+                          runHook postInstall
+                        '';
+                      };
+                  };
+              };
+            });
+
+          };
+
+        in
+        baseSet.overrideScope (lib.composeExtensions overlay pyprojectOverrides)
+      );
+
+    in
+    {
+      checks = forAllSystems (
+        system:
+        let
+          pythonSet = pythonSets.${system};
+        in
+        # Inherit tests from passthru.tests into flake checks
+        pythonSet.endoreg-db.passthru.tests
+      );
+
+
+      # Use an editable Python set for development.
+      devShells = forAllSystems (
+        system:
+        let
+          pkgs = nixpkgs.legacyPackages.${system};
+          editablePythonSet = pythonSets.${system}.overrideScope editableOverlay;
+          venv = editablePythonSet.mkVirtualEnv "endoreg-db-dev-env" {
+            endoreg-db = [ "dev" ];
+          };
+        in
+        {
+          default = pkgs.mkShell {
+            packages = [
+              venv
+              pkgs.uv
+            ];
+            env.REPO_ROOT = "$REPO_ROOT";
+
+            shellHook = ''
+              unset PYTHONPATH
+              # export REPO_ROOT=$(git rev-parse --show-toplevel)
+              export UV_NO_SYNC=1
+            '';
+          };
+          impure = pkgs.mkShell {
+            packages = [
+              pkgs.python312
+              pkgs.uv
+            ];
+            shellHook = ''
+              unset PYTHONPATH
+            '';
+          };
+        }
+      );
+
+    };
+}