Fix up poetry/flake, add stubs for some cli functions

.envrc

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

.gitignore

@@ -111,3 +111,4 @@ venv.bak/
 
 
 # End of https://www.gitignore.io/api/python
+.direnv

flake.lock

@@ -15,26 +15,75 @@
         "type": "github"
       }
     },
-    "nixpkgs": {
+    "flake-utils_2": {
       "locked": {
-        "lastModified": 1663244735,
+        "lastModified": 1659877975,
-        "narHash": "sha256-+EukKkeAx6ithOLM1u5x4D12ZFuoi6vpPYjhNDmLz1o=",
+        "narHash": "sha256-zllb8aq3YO3h8B/U0/J1WBgAL8EX5yWf5pMj3G0NAmc=",
-        "owner": "nixos",
+        "owner": "numtide",
-        "repo": "nixpkgs",
+        "repo": "flake-utils",
-        "rev": "178fea1414ae708a5704490f4c49ec3320be9815",
+        "rev": "c0e246b9b83f637f4681389ecabcb2681b4f3af0",
         "type": "github"
       },
       "original": {
-        "owner": "nixos",
+        "owner": "numtide",
-        "ref": "nixos-22.05",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1663546472,
+        "narHash": "sha256-DGYAUpehrmvyaNDWlRqSBJGfOQsavOwCc8fYgR5FIkg=",
+        "owner": "NixOS",
         "repo": "nixpkgs",
+        "rev": "1aa35f048a10cab250d038fa84311a0b589f0836",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
+      "locked": {
+        "lastModified": 1663546472,
+        "narHash": "sha256-DGYAUpehrmvyaNDWlRqSBJGfOQsavOwCc8fYgR5FIkg=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "1aa35f048a10cab250d038fa84311a0b589f0836",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "poetry2nix": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nixpkgs": "nixpkgs_2"
+      },
+      "locked": {
+        "lastModified": 1662879385,
+        "narHash": "sha256-ZmiyHn0uPH4xHYcOhY0e0sPtfyM6jCF/shmVq2aTOLc=",
+        "owner": "nix-community",
+        "repo": "poetry2nix",
+        "rev": "4f8d61cd936f853242a4ce1fd476f5488c288c26",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-community",
+        "repo": "poetry2nix",
         "type": "github"
       }
     },
     "root": {
       "inputs": {
         "flake-utils": "flake-utils",
-        "nixpkgs": "nixpkgs"
+        "nixpkgs": "nixpkgs",
+        "poetry2nix": "poetry2nix"
       }
     }
   },

flake.nix

@@ -1,41 +1,54 @@
 {
-  description = "A tool for composable tracking of scientific data provenance";
+  description = "Application packaged using poetry2nix";
 
-  inputs = {
+  inputs.flake-utils.url = "github:numtide/flake-utils";
-    nixpkgs.url = "github:nixos/nixpkgs/nixos-22.05";
+  inputs.nixpkgs.url = "github:NixOS/nixpkgs";
-    flake-utils.url = "github:numtide/flake-utils";
+  inputs.poetry2nix.url = "github:nix-community/poetry2nix";
-  };
 
-  # See https://old.reddit.com/r/Python/comments/npu66t/reproducible_python_environment_with_nix_flake/
+  outputs = { self, nixpkgs, flake-utils, poetry2nix }:
-  outputs = { self, nixpkgs, flake-utils }: 
+    {
-    flake-utils.lib.eachSystem [ "x86_64-linux" ] (system:
+      # Nixpkgs overlay providing the application
-      let
+      overlay = nixpkgs.lib.composeManyExtensions [
-        python = "python37";
+        poetry2nix.overlay
-        pkgs = (import nixpkgs {
+        (final: prev: {
-          inherit system;
+          # The application
-          config = {
+          nancy = prev.poetry2nix.mkPoetryApplication {
-            allowUnfree = true;
+            projectDir = ./.;
-            cudaSupport = true;
           };
-          overlays = [
+        })
-          ];
+      ];
-        });
+    } // (flake-utils.lib.eachDefaultSystem (system:
-        pythonPackages = pkgs.${python}.pkgs;
+      let
-        nancy = pythonPackages.buildPythonPackage {
+        pkgs = import nixpkgs {
-          name = "nancy";
+          inherit system;
-          src = ./.;
+          overlays = [ self.overlay ];
-          propagatedBuildInputs = with pythonPackages; [
-            dill
-          ];
         };
-        # core pkgs are those required to run headless scripts
+        python = pkgs.python310;
-        corePythonPkgs = ps: with ps; [
+      in
-          numpy
+      {
-          pandas
+        #apps = {
-        ];
+          #nancy = pkgs.nancy;
-        corePythonEnv = pkgs.${python}.withPackages corePythonPkgs;
+        #};
-      in rec {
+        #defaultApp = pkgs.nancy;
-        defaultPackage = nancy;
+
-        devShell = pkgs.mkShell { buildInputs = with pkgs; [ corePythonEnv ]; };
+        defaultPackage = pkgs.nancy;
-      });
+
+
+        devShell = pkgs.mkShell {
+          buildInputs = with pkgs; with python.pkgs; [
+            nixpkgs-fmt
+            poetry
+            (pkgs.poetry2nix.mkPoetryEnv {
+              inherit python;
+              projectDir = ./.;
+              pyproject = ./pyproject.toml;
+              poetrylock = ./poetry.lock;
+              editablePackageSources = {
+                nancy = ./src;
+              };
+            })
+          ];
+          shellHook = "echo 'Execute `poetry shell` to access an environment with an editable install.'";
+        };
+      }));
 }

nancy/cli/freeze.py

@@ -1,13 +0,0 @@
-import click
-
-
-@click.command()
-@click.argument("directory")
-def freeze(directory):
-    pass
-
-
-@click.command()
-@click.argument("files", nargs=-1)  # , help="Files or directories to thaw.")
-def thaw(files):
-    pass

poetry.lock

@@ -1,3 +1,40 @@
+[[package]]
+name = "attrs"
+version = "22.1.0"
+description = "Classes Without Boilerplate"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
+docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "mypy (>=0.900,!=0.940)", "pytest-mypy-plugins", "cloudpickle"]
+
+[[package]]
+name = "black"
+version = "22.8.0"
+description = "The uncompromising code formatter."
+category = "dev"
+optional = false
+python-versions = ">=3.6.2"
+
+[package.dependencies]
+click = ">=8.0.0"
+mypy-extensions = ">=0.4.3"
+pathspec = ">=0.9.0"
+platformdirs = ">=2"
+tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""}
+typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""}
+typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+colorama = ["colorama (>=0.4.3)"]
+d = ["aiohttp (>=3.7.4)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
+uvloop = ["uvloop (>=0.15.2)"]
+
 [[package]]
 name = "click"
 version = "8.1.3"
@@ -19,15 +56,18 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
-name = "dill"
+name = "coverage"
-version = "0.3.5.1"
+version = "6.4.4"
-description = "serialize all of python"
+description = "Code coverage measurement for Python"
-category = "main"
+category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
+python-versions = ">=3.7"
+
+[package.dependencies]
+tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
 
 [package.extras]
-graph = ["objgraph (>=1.7.2)"]
+toml = ["tomli"]
 
 [[package]]
 name = "importlib-metadata"
@@ -46,6 +86,160 @@ docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
 perf = ["ipython"]
 testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
 
+[[package]]
+name = "iniconfig"
+version = "1.1.1"
+description = "iniconfig: brain-dead simple config-ini parsing"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "mypy-extensions"
+version = "0.4.3"
+description = "Experimental type system extensions for programs checked with the mypy typechecker."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "packaging"
+version = "21.3"
+description = "Core utilities for Python packages"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
+
+[[package]]
+name = "pathspec"
+version = "0.10.1"
+description = "Utility library for gitignore style pattern matching of file paths."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "platformdirs"
+version = "2.5.2"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
+test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
+
+[[package]]
+name = "pluggy"
+version = "1.0.0"
+description = "plugin and hook calling mechanisms for python"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
+
+[package.extras]
+testing = ["pytest-benchmark", "pytest"]
+dev = ["tox", "pre-commit"]
+
+[[package]]
+name = "py"
+version = "1.11.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
+[[package]]
+name = "pyparsing"
+version = "3.0.9"
+description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+category = "dev"
+optional = false
+python-versions = ">=3.6.8"
+
+[package.extras]
+diagrams = ["railroad-diagrams", "jinja2"]
+
+[[package]]
+name = "pytest"
+version = "7.1.3"
+description = "pytest: simple powerful testing with Python"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+attrs = ">=19.2.0"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
+iniconfig = "*"
+packaging = "*"
+pluggy = ">=0.12,<2.0"
+py = ">=1.8.2"
+tomli = ">=1.0.0"
+
+[package.extras]
+testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
+
+[[package]]
+name = "pytest-black"
+version = "0.3.12"
+description = "A pytest plugin to enable format checking with black"
+category = "dev"
+optional = false
+python-versions = ">=2.7"
+
+[package.dependencies]
+black = {version = "*", markers = "python_version >= \"3.6\""}
+pytest = ">=3.5.0"
+toml = "*"
+
+[[package]]
+name = "pytest-cov"
+version = "3.0.0"
+description = "Pytest plugin for measuring coverage."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+coverage = {version = ">=5.2.1", extras = ["toml"]}
+pytest = ">=4.6"
+
+[package.extras]
+testing = ["virtualenv", "pytest-xdist", "six", "process-tests", "hunter", "fields"]
+
+[[package]]
+name = "toml"
+version = "0.10.2"
+description = "Python Library for Tom's Obvious, Minimal Language"
+category = "dev"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
+
+[[package]]
+name = "tomli"
+version = "2.0.1"
+description = "A lil' TOML parser"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "typed-ast"
+version = "1.5.4"
+description = "a fork of Python 2 and 3 ast modules with type comment support"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "typing-extensions"
 version = "4.3.0"
@@ -69,9 +263,38 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7"
-content-hash = "730ff71baff980650f880d17563d44d1bc64053dd792588369bc368560028cd7"
+content-hash = "49ef6dea324178124adc9639e6329fff4411087ca60907b9661d138d6b6e88aa"
 
 [metadata.files]
+attrs = [
+    {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"},
+    {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"},
+]
+black = [
+    {file = "black-22.8.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ce957f1d6b78a8a231b18e0dd2d94a33d2ba738cd88a7fe64f53f659eea49fdd"},
+    {file = "black-22.8.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5107ea36b2b61917956d018bd25129baf9ad1125e39324a9b18248d362156a27"},
+    {file = "black-22.8.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e8166b7bfe5dcb56d325385bd1d1e0f635f24aae14b3ae437102dedc0c186747"},
+    {file = "black-22.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:dd82842bb272297503cbec1a2600b6bfb338dae017186f8f215c8958f8acf869"},
+    {file = "black-22.8.0-cp310-cp310-win_amd64.whl", hash = "sha256:d839150f61d09e7217f52917259831fe2b689f5c8e5e32611736351b89bb2a90"},
+    {file = "black-22.8.0-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:a05da0430bd5ced89176db098567973be52ce175a55677436a271102d7eaa3fe"},
+    {file = "black-22.8.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4a098a69a02596e1f2a58a2a1c8d5a05d5a74461af552b371e82f9fa4ada8342"},
+    {file = "black-22.8.0-cp36-cp36m-win_amd64.whl", hash = "sha256:5594efbdc35426e35a7defa1ea1a1cb97c7dbd34c0e49af7fb593a36bd45edab"},
+    {file = "black-22.8.0-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:a983526af1bea1e4cf6768e649990f28ee4f4137266921c2c3cee8116ae42ec3"},
+    {file = "black-22.8.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3b2c25f8dea5e8444bdc6788a2f543e1fb01494e144480bc17f806178378005e"},
+    {file = "black-22.8.0-cp37-cp37m-win_amd64.whl", hash = "sha256:78dd85caaab7c3153054756b9fe8c611efa63d9e7aecfa33e533060cb14b6d16"},
+    {file = "black-22.8.0-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:cea1b2542d4e2c02c332e83150e41e3ca80dc0fb8de20df3c5e98e242156222c"},
+    {file = "black-22.8.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:5b879eb439094751185d1cfdca43023bc6786bd3c60372462b6f051efa6281a5"},
+    {file = "black-22.8.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:0a12e4e1353819af41df998b02c6742643cfef58282915f781d0e4dd7a200411"},
+    {file = "black-22.8.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c3a73f66b6d5ba7288cd5d6dad9b4c9b43f4e8a4b789a94bf5abfb878c663eb3"},
+    {file = "black-22.8.0-cp38-cp38-win_amd64.whl", hash = "sha256:e981e20ec152dfb3e77418fb616077937378b322d7b26aa1ff87717fb18b4875"},
+    {file = "black-22.8.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:8ce13ffed7e66dda0da3e0b2eb1bdfc83f5812f66e09aca2b0978593ed636b6c"},
+    {file = "black-22.8.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:32a4b17f644fc288c6ee2bafdf5e3b045f4eff84693ac069d87b1a347d861497"},
+    {file = "black-22.8.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:0ad827325a3a634bae88ae7747db1a395d5ee02cf05d9aa7a9bd77dfb10e940c"},
+    {file = "black-22.8.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:53198e28a1fb865e9fe97f88220da2e44df6da82b18833b588b1883b16bb5d41"},
+    {file = "black-22.8.0-cp39-cp39-win_amd64.whl", hash = "sha256:bc4d4123830a2d190e9cc42a2e43570f82ace35c3aeb26a512a2102bce5af7ec"},
+    {file = "black-22.8.0-py3-none-any.whl", hash = "sha256:d2c21d439b2baf7aa80d6dd4e3659259be64c6f49dfd0f32091063db0e006db4"},
+    {file = "black-22.8.0.tar.gz", hash = "sha256:792f7eb540ba9a17e8656538701d3eb1afcb134e3b45b71f20b25c77a8db7e6e"},
+]
 click = [
     {file = "click-8.1.3-py3-none-any.whl", hash = "sha256:bb4d8133cb15a609f44e8213d9b391b0809795062913b383c62be0ee95b1db48"},
     {file = "click-8.1.3.tar.gz", hash = "sha256:7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e"},
@@ -80,14 +303,139 @@ colorama = [
     {file = "colorama-0.4.5-py2.py3-none-any.whl", hash = "sha256:854bf444933e37f5824ae7bfc1e98d5bce2ebe4160d46b5edf346a89358e99da"},
     {file = "colorama-0.4.5.tar.gz", hash = "sha256:e6c6b4334fc50988a639d9b98aa429a0b57da6e17b9a44f0451f930b6967b7a4"},
 ]
-dill = [
+coverage = [
-    {file = "dill-0.3.5.1-py2.py3-none-any.whl", hash = "sha256:33501d03270bbe410c72639b350e941882a8b0fd55357580fbc873fba0c59302"},
+    {file = "coverage-6.4.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e7b4da9bafad21ea45a714d3ea6f3e1679099e420c8741c74905b92ee9bfa7cc"},
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+    {file = "typed_ast-1.5.4-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:3e123d878ba170397916557d31c8f589951e353cc95fb7f24f6bb69adc1a8a97"},
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+    {file = "typed_ast-1.5.4-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:98f80dee3c03455e92796b58b98ff6ca0b2a6f652120c263efdba4d6c5e58f72"},
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+    {file = "typed_ast-1.5.4.tar.gz", hash = "sha256:39e21ceb7388e4bb37f4c679d72707ed46c2fbf2a5609b8b8ebc4b067d977df2"},
+]
 typing-extensions = [
     {file = "typing_extensions-4.3.0-py3-none-any.whl", hash = "sha256:25642c956049920a5aa49edcdd6ab1e06d7e5d467fc00e0506c44ac86fbfca02"},
     {file = "typing_extensions-4.3.0.tar.gz", hash = "sha256:e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6"},

pyproject.toml

@@ -1,15 +1,22 @@
 [tool.poetry]
 name = "nancy"
-version = "0.0.1"
+version = "0.1.0"
 description = "Composable tracking of scientific data provenance"
 authors = ["Jacob Hinkle <jacob.hinkle@jhink.org>"]
 
 [tool.poetry.dependencies]
 python = "^3.7"
-dill = "^0.3.5"
 click = "^8.1.3"
 
 [tool.poetry.dev-dependencies]
+black = "^22.8.0"
+pytest = "^7.1.3"
+coverage = "^6.4.4"
+pytest-cov = "^3.0.0"
+pytest-black = "^0.3.12"
+
+[tool.poetry.scripts]
+nancy = "nancy.cli:main"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]

setup.cfg

@@ -1,44 +0,0 @@
-[metadata]
-name = nancy
-author = Jacob Hinkle
-author_email = hinklejd@ornl.gov
-url = https://code.ornl.gov/4jh/nancy
-keywords = data-science workflows reproducibility provenance
-version = attr:nancy.__version__
-
-[tool:pytest]
-testpaths = tests
-addopts = --verbose
-
-[aliases]
-test=pytest
-
-[options]
-packages =
-    nancy
-install_requires =
-    click
-    dill
-tests_require =
-    pytest
-python_requires = >=3.7
-
-[options.entry_points]
-console_scripts =
-    nancy = nancy.__main__:main
-
-[options.package_data]
-nancy =
-    *.sql
-
-[flake8]
-exclude = .eggs,
-          .git,
-          __pycache__,
-          nancy.egg-info,
-          build,
-          dist
-# allow a little bit longer lines than default (79)
-ignore = W504
-max-line-length= 99
-show-source = True

setup.py

@@ -1,3 +0,0 @@
-from setuptools import setup
-
-setup()

src/nancy/__init__.py

@@ -1,6 +1,6 @@
 import sqlite3
 
-from .db import init
+from . import db
 from .version import __version__
 
 
@@ -9,7 +9,16 @@ from .version import __version__
 # data by asking the user for an output dir. However, we need a database
 # initialized in order to build up the DAG in the first place, so here we
 # initialize an in-memory database to use until we have an output directory.
-_conn = init(":memory:")
+_conn = db.init(":memory:")
+
+
+def persist_db(dbpath):
+    global _conn
+
+    dst_conn = sqlite3.connect(dbpath)
+    _conn.backup(dst_conn)
+    _conn.close()
+    _conn = dst_conn
 
 
 def save_data(
@@ -30,8 +39,6 @@ def save_data(
                 "
             },
     """
-    global _conn
-
     import argparse
     import os
     import sys
@@ -55,9 +62,6 @@ def save_data(
     # Create the output directory, back up the in-memory db to this location, an
     # switch to it.
     os.makedirs(args.out_dir, exist_ok=True)
-    dst_conn = sqlite3.connect(os.path.join(args.out_dir, "prov.db"))
+    persist_db(os.path.join(args.out_dir, "nancy.db"))
-    _conn.backup(dst_conn)
-    _conn.close()
-    _conn = dst_conn
 
     # Now we save the provided roots, and record their locations in _conn.data

src/nancy/cli/freeze.py

@@ -0,0 +1,28 @@
+import click
+
+from .. import store
+
+
+@click.command()
+@click.argument("directory")
+def freeze(directory):
+    if not os.path.isdir(directory):
+        raise ValueError(f"Cannot freeze non-existent directory {directory}")
+
+    existing_store = db.find_store(directory)
+    if existing_store is None:  # this is a new store
+        s = store.init(directory)
+    else:  # this is an existing store
+        store.connect(directory)
+
+    # remove write permissions on all files except nancy.db
+
+    # compute checksums on all files, update versions in nancy.db as appropriate
+
+    # remove write permissions on nancy.db
+
+
+@click.command()
+@click.argument("files", nargs=-1)  # , help="Files or directories to thaw.")
+def thaw(files):
+    pass

src/nancy/schema.sql

@@ -4,6 +4,31 @@ PRAGMA user_version=0; -- version of this schema.
 
 PRAGMA foreign_keys=ON;
 
+-- Stores, directories, and files
+-- These are the primary objects tracked by nancy.
+-- A store is a directory containing a file called nancy.db
+CREATE TABLE store (id INTEGER PRIMARY KEY NOT NULL,
+    name TEXT,
+    dbpath TEXT NOT NULL
+);
+-- Within the store are directories that contain files.
+CREATE TABLE store_directory (id INTEGER PRIMARY KEY NOT NULL,
+    store INTEGER NOT NULL,
+    relpath TEXT,
+    frozen BOOL NOT NULL,
+    FOREIGN KEY (store) REFERENCES store (id)
+);
+CREATE TABLE store_file (id INTEGER PRIMARY KEY NOT NULL,
+    directory INTEGER NOT NULL,
+    relpath TEXT,  -- path relative to top-level of _store_, not dir
+    frozen BOOL NOT NULL,
+
+    source_datum INTEGER,
+
+    FOREIGN KEY (directory) REFERENCES store_directory (id)
+    FOREIGN KEY (source_datum) REFERENCES datum (id)
+);
+
 -- computational environment which can execute "runs"
 CREATE TABLE environment (id INTEGER PRIMARY KEY NOT NULL,
     hostname TEXT, -- platform.node(): computer's network name
@@ -18,7 +43,7 @@ CREATE TABLE environment (id INTEGER PRIMARY KEY NOT NULL,
 -- It corresponds to a single host process. Note that if multiple calls to
 -- nancy.run() are provided within a single python script, multiple "processes"
 -- may be created.  Also note that historical processes are automatically
--- imported and merged when possible when loading "data" from disk.
+-- imported and merged when possible when loading a "datum" from disk.
 CREATE TABLE process (id INTEGER PRIMARY KEY NOT NULL,
     -- we use POSIX timestamps in UTC for time recording.
     -- e.g. datetime.datetime.now().timestamp()
@@ -94,8 +119,8 @@ CREATE TABLE task(id INTEGER PRIMARY KEY NOT NULL,
 );
 -- A datum is an object that is computed as the output of a task, given as a
 -- literal value in a config file, or loaded from a file.
-CREATE TABLE data(id INTEGER PRIMARY KEY NOT NULL,
+CREATE TABLE datum(id INTEGER PRIMARY KEY NOT NULL,
-     -- provider_type describes where the data came from. Choices are:
+     -- provider_type describes where the datum came from. Choices are:
      --   - COMPUTED: output of a decorated Function
      --   - IMPORTED: imported output from a prior process
      --   - LITERAL: literal value provided in a config file

src/nancy/store.py

@@ -0,0 +1,20 @@
+"""Utilities for creating new stores and linking between them."""
+
+import os
+
+
+def find_store(path):
+    """
+    Given a path, find a store dir containing nancy.db at any level above it.
+    """
+    d = os.path.realpath(path)  # dereference any symlinks in path
+    while True:
+        if os.path.exists(os.path.join(d, "nancy.db")):
+            return d
+        newd = os.path.dirname(path)
+        if newd == d:  # indicates this is a filesystem root like C:\ or /
+            return None
+
+
+def connect(path):
+    """Given directory, connect to its store"""