diff --git a/flake.nix b/flake.nix index aaeaf99..0962057 100644 --- a/flake.nix +++ b/flake.nix @@ -1,14 +1,64 @@ { - description = "A collection of flake templates"; - - outputs = { self }: { - templates = { - portrait = { - path = ./libs/jump_portrait; - description = "JUMP portrait development template"; - }; - - }; - + inputs = { + nixpkgs.url = "github:NixOS/nixpkgs/nixos-24.05"; + nixpkgs_master.url = "github:NixOS/nixpkgs/master"; + systems.url = "github:nix-systems/default"; + devenv.url = "github:cachix/devenv"; + }; + nixConfig = { + extra-trusted-public-keys = "devenv.cachix.org-1:w1cLUi8dv3hnoSPGAuibQv+f9TZLr6cv/Hm9XgU50cw="; + extra-substituters = "https://devenv.cachix.org"; }; -} + outputs = { self, nixpkgs, devenv, systems, ... } @ inputs: + let + forEachSystem = nixpkgs.lib.genAttrs (import systems); + in + { + packages = forEachSystem (system: { + devenv-up = self.devShells.${system}.default.config.procfileScript; + }); + devShells = forEachSystem + (system: + let + pkgs = import nixpkgs { + system = system; + config.allowUnfree = true; + }; + mpkgs = import inputs.nixpkgs_master { + system = system; + config.allowUnfree = true; + }; + in + { + default = devenv.lib.mkShell { + inherit inputs pkgs; + modules = [ + { + stdenv = pkgs.clangStdenv; + env.NIX_LD = nixpkgs.lib.fileContents "${pkgs.stdenv.cc}/nix-support/dynamic-linker"; + env.NIX_LD_LIBRARY_PATH = nixpkgs.lib.makeLibraryPath (with pkgs; [ + # Add needed packages here + pkgs.libz # for numpy + pkgs.stdenv.cc.cc + pkgs.libGL + ]); + # https://devenv.sh/reference/options/ + packages = with pkgs; [ + poetry + python311 + ruff + pyright + ]; + enterShell = '' + export LD_LIBRARY_PATH=$NIX_LD_LIBRARY_PATH + export PYTHON_KEYRING_BACKEND=keyring.backends.fail.Keyring + if [ ! -d ".venv" ]; then + poetry install -vv --with dev --no-root + fi + source .venv/bin/activate + ''; + } + ]; + }; + }); + }; diff --git a/libs/jump_babel/.envrc b/libs/jump_babel/.envrc index cffc922..f990172 100644 --- a/libs/jump_babel/.envrc +++ b/libs/jump_babel/.envrc @@ -1 +1 @@ -use flake . --impure +use flake . --impure --accept-flake-config diff --git a/libs/jump_portrait/.envrc b/libs/jump_portrait/.envrc index a5dbbcb..cffc922 100644 --- a/libs/jump_portrait/.envrc +++ b/libs/jump_portrait/.envrc @@ -1 +1 @@ -use flake . +use flake . --impure diff --git a/libs/jump_portrait/flake.lock b/libs/jump_portrait/flake.lock index 534e58b..bfb1572 100644 --- a/libs/jump_portrait/flake.lock +++ b/libs/jump_portrait/flake.lock @@ -83,26 +83,6 @@ "type": "github" } }, - "dream2nix": { - "inputs": { - "nixpkgs": "nixpkgs_3", - "purescript-overlay": "purescript-overlay", - "pyproject-nix": "pyproject-nix" - }, - "locked": { - "lastModified": 1721316623, - "narHash": "sha256-WmPX3r0YtUxvcQmTgvNld2xJooWr4f/+5dURiw7/3zc=", - "owner": "nix-community", - "repo": "dream2nix", - "rev": "4e9fd61a1201f4b3800d6946810a6b4c2ecdcde8", - "type": "github" - }, - "original": { - "owner": "nix-community", - "repo": "dream2nix", - "type": "github" - } - }, "flake-compat": { "flake": false, "locked": { @@ -171,24 +151,6 @@ "type": "github" } }, - "flake-utils_3": { - "inputs": { - "systems": "systems_3" - }, - "locked": { - "lastModified": 1710146030, - "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=", - "owner": "numtide", - "repo": "flake-utils", - "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a", - "type": "github" - }, - "original": { - "owner": "numtide", - "repo": "flake-utils", - "type": "github" - } - }, "gitignore": { "inputs": { "nixpkgs": [ @@ -370,16 +332,16 @@ }, "nixpkgs_3": { "locked": { - "lastModified": 1720181791, - "narHash": "sha256-i4vJL12/AdyuQuviMMd1Hk2tsGt02hDNhA0Zj1m16N8=", + "lastModified": 1720535198, + "narHash": "sha256-zwVvxrdIzralnSbcpghA92tWu2DV2lwv89xZc8MTrbg=", "owner": "NixOS", "repo": "nixpkgs", - "rev": "4284c2b73c8bce4b46a6adf23e16d9e2ec8da4bb", + "rev": "205fd4226592cc83fd4c0885a3e4c9c400efabb5", "type": "github" }, "original": { "owner": "NixOS", - "ref": "nixpkgs-unstable", + "ref": "nixos-23.11", "repo": "nixpkgs", "type": "github" } @@ -453,78 +415,12 @@ "type": "github" } }, - "purescript-overlay": { - "inputs": { - "nixpkgs": [ - "dream2nix", - "nixpkgs" - ], - "slimlock": "slimlock" - }, - "locked": { - "lastModified": 1696022621, - "narHash": "sha256-eMjFmsj2G1E0Q5XiibUNgFjTiSz0GxIeSSzzVdoN730=", - "owner": "thomashoneyman", - "repo": "purescript-overlay", - "rev": "047c7933abd6da8aa239904422e22d190ce55ead", - "type": "github" - }, - "original": { - "owner": "thomashoneyman", - "repo": "purescript-overlay", - "type": "github" - } - }, - "pyproject-nix": { - "flake": false, - "locked": { - "lastModified": 1702448246, - "narHash": "sha256-hFg5s/hoJFv7tDpiGvEvXP0UfFvFEDgTdyHIjDVHu1I=", - "owner": "davhau", - "repo": "pyproject.nix", - "rev": "5a06a2697b228c04dd2f35659b4b659ca74f7aeb", - "type": "github" - }, - "original": { - "owner": "davhau", - "ref": "dream2nix", - "repo": "pyproject.nix", - "type": "github" - } - }, "root": { "inputs": { "devenv": "devenv", - "dream2nix": "dream2nix", - "flake-utils": "flake-utils_3", - "nixpkgs": [ - "dream2nix", - "nixpkgs" - ], + "nixpkgs": "nixpkgs_3", "nixpkgs_master": "nixpkgs_master", - "systems": "systems_4" - } - }, - "slimlock": { - "inputs": { - "nixpkgs": [ - "dream2nix", - "purescript-overlay", - "nixpkgs" - ] - }, - "locked": { - "lastModified": 1688610262, - "narHash": "sha256-Wg0ViDotFWGWqKIQzyYCgayeH8s4U1OZcTiWTQYdAp4=", - "owner": "thomashoneyman", - "repo": "slimlock", - "rev": "b5c6cdcaf636ebbebd0a1f32520929394493f1a6", - "type": "github" - }, - "original": { - "owner": "thomashoneyman", - "repo": "slimlock", - "type": "github" + "systems": "systems_3" } }, "systems": { @@ -571,21 +467,6 @@ "repo": "default", "type": "github" } - }, - "systems_4": { - "locked": { - "lastModified": 1681028828, - "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=", - "owner": "nix-systems", - "repo": "default", - "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", - "type": "github" - }, - "original": { - "owner": "nix-systems", - "repo": "default", - "type": "github" - } } }, "root": "root", diff --git a/libs/jump_portrait/flake.nix b/libs/jump_portrait/flake.nix index c153d9e..ddcff96 100644 --- a/libs/jump_portrait/flake.nix +++ b/libs/jump_portrait/flake.nix @@ -1,62 +1,69 @@ + { inputs = { - dream2nix.url = "github:nix-community/dream2nix"; - nixpkgs.follows = "dream2nix/nixpkgs"; + nixpkgs.url = "github:NixOS/nixpkgs/nixos-23.11"; nixpkgs_master.url = "github:NixOS/nixpkgs/master"; - flake-utils.url = "github:numtide/flake-utils"; systems.url = "github:nix-systems/default"; devenv.url = "github:cachix/devenv"; }; - outputs = { self, nixpkgs, devenv, systems, dream2nix, ... } @ inputs: - inputs.flake-utils.lib.eachDefaultSystem (system: - let - - pkgs = import nixpkgs { - system = system; - config.allowUnfree = true; - }; + nixConfig = { + extra-trusted-public-keys = "devenv.cachix.org-1:w1cLUi8dv3hnoSPGAuibQv+f9TZLr6cv/Hm9XgU50cw="; + extra-substituters = "https://devenv.cachix.org"; + }; - mpkgs = import inputs.nixpkgs_master { - system = system; - config.allowUnfree = true; - }; + outputs = { self, nixpkgs, devenv, systems, ... } @ inputs: + let + forEachSystem = nixpkgs.lib.genAttrs (import systems); + in + { + packages = forEachSystem (system: { + devenv-up = self.devShells.${system}.default.config.procfileScript; + }); - in { - devShells = + devShells = forEachSystem + (system: let - python_with_pkgs = (pkgs.python310.withPackages(pp: [])); + pkgs = import nixpkgs { + system = system; + config.allowUnfree = true; + }; + + mpkgs = import inputs.nixpkgs_master { + system = system; + config.allowUnfree = true; + }; in - with pkgs; - { - default = pkgs.mkShell { - NIX_LD = runCommand "ld.so" {} '' - ln -s "$(cat '${pkgs.stdenv.cc}/nix-support/dynamic-linker')" $out - ''; - NIX_LD_LIBRARY_PATH = lib.makeLibraryPath [ - pkgs.zlib - ]; - packages = [ - mpkgs.rye - uv - ]; - venvDir = "./.venv"; - postVenvCreation = '' - unset SOURCE_DATE_EPOCH - ''; - postShellHook = '' - unset SOURCE_DATE_EPOCH - ''; - shellHook = '' - export LD_LIBRARY_PATH=$NIX_LD_LIBRARY_PATH:"${pkgs.stdenv.cc.cc.lib}/lib" - export PYTHON_KEYRING_BACKEND=keyring.backends.fail.Keyring - runHook venvShellHook - export PYTHONPATH=${python_with_pkgs}/${python_with_pkgs.sitePackages}:$PYTHONPATH - rye sync - source .venv/bin/activate - ''; - }; + { + default = devenv.lib.mkShell { + inherit inputs pkgs; + modules = [ + { + stdenv = pkgs.clangStdenv; + env.NIX_LD = nixpkgs.lib.fileContents "${pkgs.stdenv.cc}/nix-support/dynamic-linker"; + env.NIX_LD_LIBRARY_PATH = nixpkgs.lib.makeLibraryPath (with pkgs; [ + # Add needed packages here + pkgs.libz # for numpy + pkgs.stdenv.cc.cc + pkgs.libGL + ]); + # https://devenv.sh/reference/options/ + packages = with pkgs; [ + poetry + ruff + python310 + ]; + enterShell = '' + export LD_LIBRARY_PATH=$NIX_LD_LIBRARY_PATH + export 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b/libs/jump_portrait/pyproject.toml index f284dbe..933c1a1 100644 --- a/libs/jump_portrait/pyproject.toml +++ b/libs/jump_portrait/pyproject.toml @@ -1,53 +1,35 @@ -[project] +[tool.poetry] name = "jump_portrait" version = "0.0.22" description = "Tools to fetch and visualize JUMP images" -authors = [{ name = "Alán Muñoz", email = "amunozgo@broadinstitute.org" }] readme = "README.md" -requires-python = ">=3.10,<3.12" -dependencies = [ - "boto3>=1.33.1", - "broad-babel>=0.1.22", - "joblib~=1.3.2", - "matplotlib~=3.8.2", - "polars>=0.19.19", - "pooch~=1.7.0", - "pyarrow>=14.0.1", - "s3path~=0.5.0", - "tqdm~=4.66.1", - "s3fs~=2024.6.0", - "jupyter>=1.0.0", - "numpy<2.0.0", -] -license = { text = "MIT" } +authors = ["Alan Munoz"] +packages = [{include = "jump_portrait", from= "src"}] -[project.optional-dependencies] -dev = [ -"jupyter~=1.0.0", -"pytest>=8.2.2", -"jupytext~=1.15.0", -"ruff-lsp~=0.0.48", -"ruff~=0.3.2", -"ipdb>=0.13.13", -] +[tool.poetry.dependencies] +python = ">=3.10,<3.12" +boto3 = ">=1.33.1" +broad-babel = ">=0.1.22" +joblib = "^1.3.2" +matplotlib = "^3.8.2" +polars = "^0.19.19" +pooch = "^1.7.0" +pyarrow = ">=14.0.1" +s3path = "^0.5.0" +tqdm = "^4.66.1" +s3fs = "^2024.6.0" -[build-system] -# setuptools>=61 supports PEPs 517, 518, 621, 660 -# https://setuptools.pypa.io/en/latest/history.html#v61-0-0 -# setuptools-scm asks for setuptools>=64 -# https://setuptools-scm.readthedocs.io/en/latest/ -requires = ["setuptools>=64.0.0", "setuptools-scm>=8.0"] -build-backend = "setuptools.build_meta" +[tool.poetry.group.dev.dependencies] +jupyter = "^1.0.0" +jupytext = "^1.15.0" +pytest = "^7.4.1" +# ruff-lsp = "^0.0.48" +# ruff = "^0.3.2" +ipdb = "^0.13.13" -[tool] -rye = { dev-dependencies = [ - "pytest>=8.2.2", - "jupyter~=1.0.0", - "ruff-lsp~=0.0.48", - "ruff~=0.3.2", - "ipdb~=0.13.13", - "jupytext~=1.15.0", -] } +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" [tool.ruff] select = ["ANN", "C90", "D", "E", "F", "I", "N", "NPY", "PTH", "TID", "UP", "W"] diff --git a/libs/jump_portrait/src/jump_portrait/fetch.py b/libs/jump_portrait/src/jump_portrait/fetch.py index 4774161..7d71b16 100644 --- a/libs/jump_portrait/src/jump_portrait/fetch.py +++ b/libs/jump_portrait/src/jump_portrait/fetch.py @@ -27,8 +27,8 @@ get_image_from_s3uri, read_parquet_s3, ) -from jump_portrait.utils import batch_processing, parallel - +from jump_portrait.utils import batch_processing, parallel, try_function +from itertools import groupby, product, starmap def format_cellpainting_s3() -> str: return ( @@ -84,8 +84,8 @@ def get_jump_image( Site identifier (also called foci), default is 1. correction : str Whether or not to use corrected data. It does not by default. - apply_illum : bool - When correction=="Illum" apply Illum correction on original image. + apply_correction : bool + When apply_correction=="Illum" apply Illum correction on original image. Returns ------- @@ -119,6 +119,46 @@ def get_jump_image( return result +def get_jump_image_batch(metadata: pl.DataFrame, channel: list[str], + site: list[str], correction:str='Orig', + verbose: bool=True, + ) -> (pl.DataFrame, list[tuple]): + ''' + Load jump image associated to metadata in a threaded fashion. + + Parameters: + ---------- + metadata : pl.DataFrame + must have the column in this specific order ("Metadata_Source", "Metadata_Batch", "Metadata_Plate", "Metadata_Well") + channel : list of string + list of channel desired + Must be in ['DNA', 'ER', 'AGP', 'Mito', 'RNA'] + site : list of string + list of site desired + - For compound, must be in ['1' - '6'] + - For ORF, CRISPR, must be in ['1' - '9'] + correction : str + Must be 'Illum' or 'Orig' + verbose : bool + Whether to enable tqdm or not. + + Return: + ---------- + iterable : list of tuple + list containing the metadata, channel, site and correction + img_list : list of array + list containing the images + + ''' + iterable = list(starmap(lambda *x: (*x[0], *x[1:]), product(metadata.rows(), channel, site, [correction]))) + img_list = parallel(iterable, batch_processing(try_function(get_jump_image)), + verbose=verbose) + + return iterable, img_list + + + + def get_item_location_metadata( item_name: str, operator: str or None = None, @@ -322,3 +362,11 @@ def get_gene_images( ) return images + +metadata_pre = get_item_location_info("MYT1") +iterable, img_list = get_jump_image_batch(metadata_pre.select(pl.col( +["Metadata_Source", "Metadata_Batch", "Metadata_Plate", "Metadata_Well"])), + channel=['DNA','ER', 'RNA'],#, 'ER', 'AGP', 'Mito', 'RNA'], + site=[str(i) for i in range(8)], + correction='Orig', + verbose=False) #None, 'Illum' diff --git a/libs/jump_portrait/src/jump_portrait/utils.py b/libs/jump_portrait/src/jump_portrait/utils.py index d9f680d..7f54038 100644 --- a/libs/jump_portrait/src/jump_portrait/utils.py +++ b/libs/jump_portrait/src/jump_portrait/utils.py @@ -5,7 +5,7 @@ from typing import Any from joblib import Parallel, cpu_count, delayed - +from tqdm import tqdm def slice_iterable(iterable: Iterable[Any], count: int) -> list[slice]: """Create slices of the given iterable. @@ -41,6 +41,7 @@ def parallel( args: list[Any] = [], jobs: int = None, timeout: float = None, + verbose: bool = True, **kwargs: dict[Any, Any], ) -> list[Any]: """Distribute process on iterable. @@ -57,6 +58,8 @@ def parallel( Number of jobs to launch, by default None timeout: float, optional Timeout for worker processes. + verbose: bool, optional + Whether to enable tqdm or not. Returns ------- @@ -72,7 +75,7 @@ def parallel( jobs = len(iterable) slices = slice_iterable(iterable, jobs) result = Parallel(n_jobs=jobs, timeout=timeout)( - delayed(func)(chunk, idx, *args, **kwargs) + delayed(func)(chunk, idx, verbose, *args, **kwargs) for idx, chunk in enumerate([iterable[s] for s in slices]) ) @@ -82,13 +85,34 @@ def parallel( def batch_processing(f: Callable): # This assumes parameters are packed in a tuple - def batched_fn(item_list: Iterable, job_idx: int, *args, **kwargs): + def batched_fn(item_list: Iterable, job_idx: int, + verbose:bool=True, + *args, **kwargs): results = [] - for item in item_list: - # pbar.set_description(f"Processing {item}") + for item in tqdm(item_list, position=0, leave=True, + disable=not verbose, + desc=f"worker #{job_idx}"): results.append(f(*item, *args, **kwargs)) if any([x is not None for x in results]): return results return batched_fn + + +def try_function(f: Callable): + ''' + Wrap a function into an instance which will Try to call the function: + If it success, return the output of the function. + If it fails, return None + ''' + # This assumes parameters are packed in a tuple + def batched_fn(*item, **kwargs): + try: + result = f(*item, **kwargs) + + except: + result = None + + return result + return batched_fn