From 9e7af6b8a13b1746429cdd4092296372fe86e0e3 Mon Sep 17 00:00:00 2001 From: Jacob Hinkle Date: Mon, 19 Sep 2022 09:31:41 -0400 Subject: [PATCH] Fix up poetry/flake, add stubs for some cli functions --- .envrc | 1 + .gitignore | 1 + flake.lock | 67 ++++- flake.nix | 83 +++--- nancy/cli/freeze.py | 13 - poetry.lock | 368 ++++++++++++++++++++++++++- pyproject.toml | 11 +- setup.cfg | 44 ---- setup.py | 3 - {nancy => src/nancy}/__init__.py | 20 +- {nancy => src/nancy}/__main__.py | 0 {nancy => src/nancy}/cli/__init__.py | 0 src/nancy/cli/freeze.py | 28 ++ {nancy => src/nancy}/db.py | 0 {nancy => src/nancy}/schema.sql | 31 ++- src/nancy/store.py | 20 ++ {nancy => src/nancy}/version.py | 0 17 files changed, 563 insertions(+), 127 deletions(-) create mode 100644 .envrc delete mode 100644 nancy/cli/freeze.py delete mode 100644 setup.cfg delete mode 100644 setup.py rename {nancy => src/nancy}/__init__.py (91%) rename {nancy => src/nancy}/__main__.py (100%) rename {nancy => src/nancy}/cli/__init__.py (100%) create mode 100644 src/nancy/cli/freeze.py rename {nancy => src/nancy}/db.py (100%) rename {nancy => src/nancy}/schema.sql (84%) create mode 100644 src/nancy/store.py rename {nancy => src/nancy}/version.py (100%) diff --git a/.envrc b/.envrc new file mode 100644 index 0000000..3550a30 --- /dev/null +++ b/.envrc @@ -0,0 +1 @@ +use flake diff --git a/.gitignore b/.gitignore index a1adbbe..ee2c222 100644 --- a/.gitignore +++ b/.gitignore @@ -111,3 +111,4 @@ venv.bak/ # End of https://www.gitignore.io/api/python +.direnv diff --git a/flake.lock b/flake.lock index 0b9b9d1..4030e9c 100644 --- a/flake.lock +++ b/flake.lock @@ -15,26 +15,75 @@ "type": "github" } }, - "nixpkgs": { + "flake-utils_2": { "locked": { - "lastModified": 1663244735, - "narHash": "sha256-+EukKkeAx6ithOLM1u5x4D12ZFuoi6vpPYjhNDmLz1o=", - "owner": "nixos", - "repo": "nixpkgs", - "rev": "178fea1414ae708a5704490f4c49ec3320be9815", + "lastModified": 1659877975, + "narHash": "sha256-zllb8aq3YO3h8B/U0/J1WBgAL8EX5yWf5pMj3G0NAmc=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "c0e246b9b83f637f4681389ecabcb2681b4f3af0", "type": "github" }, "original": { - "owner": "nixos", - "ref": "nixos-22.05", + "owner": "numtide", + "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" } } }, diff --git a/flake.nix b/flake.nix index 0c3edc8..2c4bf41 100644 --- a/flake.nix +++ b/flake.nix @@ -1,41 +1,54 @@ { - description = "A tool for composable tracking of scientific data provenance"; + description = "Application packaged using poetry2nix"; - inputs = { - nixpkgs.url = "github:nixos/nixpkgs/nixos-22.05"; - flake-utils.url = "github:numtide/flake-utils"; - }; + inputs.flake-utils.url = "github:numtide/flake-utils"; + inputs.nixpkgs.url = "github:NixOS/nixpkgs"; + 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 }: - flake-utils.lib.eachSystem [ "x86_64-linux" ] (system: - let - python = "python37"; - pkgs = (import nixpkgs { - inherit system; - config = { - allowUnfree = true; - cudaSupport = true; + outputs = { self, nixpkgs, flake-utils, poetry2nix }: + { + # Nixpkgs overlay providing the application + overlay = nixpkgs.lib.composeManyExtensions [ + poetry2nix.overlay + (final: prev: { + # The application + nancy = prev.poetry2nix.mkPoetryApplication { + projectDir = ./.; }; - overlays = [ - ]; - }); - pythonPackages = pkgs.${python}.pkgs; - nancy = pythonPackages.buildPythonPackage { - name = "nancy"; - src = ./.; - propagatedBuildInputs = with pythonPackages; [ - dill - ]; + }) + ]; + } // (flake-utils.lib.eachDefaultSystem (system: + let + pkgs = import nixpkgs { + inherit system; + overlays = [ self.overlay ]; }; - # core pkgs are those required to run headless scripts - corePythonPkgs = ps: with ps; [ - numpy - pandas - ]; - corePythonEnv = pkgs.${python}.withPackages corePythonPkgs; - in rec { - defaultPackage = nancy; - devShell = pkgs.mkShell { buildInputs = with pkgs; [ corePythonEnv ]; }; - }); + python = pkgs.python310; + in + { + #apps = { + #nancy = pkgs.nancy; + #}; + #defaultApp = pkgs.nancy; + + 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.'"; + }; + })); } diff --git a/nancy/cli/freeze.py b/nancy/cli/freeze.py deleted file mode 100644 index 41e530b..0000000 --- a/nancy/cli/freeze.py +++ /dev/null @@ -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 diff --git a/poetry.lock b/poetry.lock index ea27c07..044f84c 100644 --- a/poetry.lock +++ b/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 = 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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 = 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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 diff --git a/setup.py b/setup.py deleted file mode 100644 index 6068493..0000000 --- a/setup.py +++ /dev/null @@ -1,3 +0,0 @@ -from setuptools import setup - -setup() diff --git a/nancy/__init__.py b/src/nancy/__init__.py similarity index 91% rename from nancy/__init__.py rename to src/nancy/__init__.py index e13c4f6..ae6edc8 100644 --- a/nancy/__init__.py +++ b/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")) - _conn.backup(dst_conn) - _conn.close() - _conn = dst_conn + persist_db(os.path.join(args.out_dir, "nancy.db")) # Now we save the provided roots, and record their locations in _conn.data diff --git a/nancy/__main__.py b/src/nancy/__main__.py similarity index 100% rename from nancy/__main__.py rename to src/nancy/__main__.py diff --git a/nancy/cli/__init__.py b/src/nancy/cli/__init__.py similarity index 100% rename from nancy/cli/__init__.py rename to src/nancy/cli/__init__.py diff --git a/src/nancy/cli/freeze.py b/src/nancy/cli/freeze.py new file mode 100644 index 0000000..77c2a7d --- /dev/null +++ b/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 diff --git a/nancy/db.py b/src/nancy/db.py similarity index 100% rename from nancy/db.py rename to src/nancy/db.py diff --git a/nancy/schema.sql b/src/nancy/schema.sql similarity index 84% rename from nancy/schema.sql rename to src/nancy/schema.sql index 0417674..51390cb 100644 --- a/nancy/schema.sql +++ b/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, - -- provider_type describes where the data came from. Choices are: +CREATE TABLE datum(id INTEGER PRIMARY KEY NOT NULL, + -- 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 diff --git a/src/nancy/store.py b/src/nancy/store.py new file mode 100644 index 0000000..0c28a50 --- /dev/null +++ b/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""" diff --git a/nancy/version.py b/src/nancy/version.py similarity index 100% rename from nancy/version.py rename to src/nancy/version.py