Update readme descriptions

.envrc

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+# ^ added for shellcheck and file-type detection
+
+# Reload if any of these files change
+watch_file .envrc.local
+
+if [[ $(type -t use_flake) != function ]]; then
+  echo "ERROR: use_flake function missing."
+  echo "Please update direnv to v2.30.0 or later."
+  exit 1
+fi
+
+if [ -f .envrc.local ]; then
+  source_env .envrc.local
+
+  export NIX_CONFIG="access-tokens = github.com=$NIX_GITHUB_TOKEN"
+else
+  echo "
+WARNING: .envrc.local not found, please run \`cp .envrc.local.template .envrc.local\`  
+and fill in the missing values."
+fi
+
+use_flake

.envrc.local.template

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+# This value is a GitHub PAT, it can be generated on the following page:
+# https://github.com/settings/tokens
+#
+# Ensure the "repo" scope is enabled
+export NIX_GITHUB_TOKEN=<TODO>
+

.gitignore

@@ -1,2 +1,4 @@
 result
 result-*
+.ipynb_checkpoints/
+.envrc.local

README.md

@@ -41,9 +41,39 @@ To access the `lib` code exported by this flake, declare this repo as a flake in
 
 ## Packages
 
-### `.#sppl`
+List of Nix packages available in this repo.
+
+### `.#baseOCI`
+
+### `.#loomOCI`
+
+A Loom container image is also provided. It can be built and loaded into your local Docker registry with the following command:
+
+```console
+$ docker load -i $(nix build '.#loomOCI' --no-link --print-out-paths)
+```
+
+### `.#jupyter-bayes3d`
+
+A jupyter environment with bayes libraries available.
+
+Example:
+```console
+$ nix run .#jupyter-bayes3d notebook ./notebooks/demo.ipynb
+```
+
+## Python Packages
+
+Here are all the python packages this flake provides, on top of all the ones
+available in nixpkgs.
+
+All the packages are compiled against Python 3.11.
+
+### `.#bayes3d`
 
-Python [library by ProbSys](https://github.com/probsys/sppl) packaged for python3.9 .
+Bayes3D is a 3D scene perception system based on probabilistic inverse graphics.
+
+* [GitHub](https://github.com/probcomp/bayes3d)
 
 ### `.#loom`
 
@@ -52,27 +82,101 @@ platform-dependent `distributions`.
 
 Your options are:
 
-```bash
-nix build '.#packages.x86_64-linux.loom'                      # same as `.#loom` if that is your OS/arch
-nix build './envs-flake#packages.x86_64-darwin.ociImgLoom'
+```console
+$ nix build '.#packages.x86_64-linux.loom'                      # same as `.#loom` if that is your OS/arch
+$ nix build './envs-flake#packages.x86_64-darwin.ociImgLoom'
 ```
 
 If you are running on Mac silicon (`aarch64-darwin`), that OCI image will run but behavior is not defined or supported.
 
-#### `.#loom.morePackages.distributions`
+### `.#distinctipy`
+
+distinctipy is a lightweight python package providing functions to generate colours that are visually distinct from one another.
+
+* [GitHub](https://github.com/alan-turing-institute/distinctipy)
+* [PyPi](https://pypi.org/project/distinctipy)
+
+### `.#distributions`
 
 Native library for probability distributions in python used by Loom. NOTE: this ONLY builds for `x86_64` architectures and only runs on linux.
 
-#### `.#loom.morePackages.parsable`
-#### `.#loom.morePackages.pymetis`
-#### `.#loom.morePackages.goftests`
-#### `.#loom.morePackages.tcmalloc`
+* [GitHub](https://github.com/posterior/distributions)
 
-Other upstream python packages required by Distributions and/or Loom.
+### `.#dm-tree`
 
-#### `.#loom.ociImg`
+Tree is a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each "leaf" preserving the overall structure.
 
-A Loom container image is also provided as a passthru attribute of `loom`. It can be built and loaded into your local Docker registry with the following command:
-```sh
-docker load -i $(nix build 'github:OpenGen/nix/loom-oci-img-attribute#loom.ociImg' --no-link --print-out-paths)
-```
+* [GitHub](https://github.com/deepmind/tree)
+* [PyPi](https://pypi.org/project/dm-tree)
+
+### `.#genjax`
+
+GenJAX is an implementation of Gen on top of JAX - exposing the ability to programmatically construct and manipulate generative functions, as well as JIT compile + auto-batch inference computations using generative functions onto GPU devices.
+
+* [GitHub](https://github.com/probcomp/genjax)
+
+### `.#goftests`
+
+Goftests is intended for unit testing random samplers that generate arbitrary plain-old-data, and focuses on robustness rather than statistical efficiency. In contrast to scipy.stats and statsmodels, goftests does not make assumptions on the distribution being tested, and requires only a simple (sample, prob) interface provided by MCMC samplers.
+
+* [GitHub](https://github.com/posterior/goftests)
+
+### `.#open3d`
+
+Open3D is an open-source library that supports rapid development of software that deals with 3D data.
+
+* [GitHub](https://github.com/isl-org/Open3D)
+* [PyPi](https://pypi.org/project/open3d)
+
+### `.#opencv-python`
+
+Wrapper package for OpenCV python bindings.
+
+* [GitHub](https://github.com/opencv/opencv-python)
+* [PyPi](https://pypi.org/project/opencv-python)
+
+### `.#oryx`
+
+Oryx is a library for probabilistic programming and deep learning built on top of Jax.
+
+* [GitHub](https://github.com/jax-ml/oryx)
+* [PyPi](https://pypi.org/project/oryx)
+
+### `.#parsable`
+
+Parsable is a lightweight decorator-based command line parser library. Parsable was written to be simpler than argparse, optparse, and argh.
+
+### `.#plum-dispatch`
+
+Multiple dispatch in Python.
+
+* [GitHub](https://github.com/beartype/plum)
+* [PyPi](https://pypi.org/project/plum-dispatch)
+
+### `.#pymetis`
+
+PyMetis is a Python wrapper for the Metis graph partititioning software.
+
+* [GitHub](https://github.com/inducer/pymetis)
+* [PyPi](https://pypi.org/project/PyMetis)
+
+### `.#pyransac3d`
+
+pyRANSAC-3D is an open source implementation of Random sample consensus (RANSAC) method. It fits primitive shapes such as planes, cuboids and cylinder in a point cloud to many aplications: 3D slam, 3D reconstruction, object tracking and many others.
+
+* [GitHub](https://github.com/leomariga/pyRANSAC-3D)
+* [PyPi](https://pypi.org/project/pyransac3d)
+
+### `.#sppl`
+
+Probabilistic programming system for fast and exact symbolic inference.
+
+* [GitHub](https://github.com/probsys/sppl)
+* [PyPi](https://pypi.org/project/sppl)
+
+### `.#tensorflow-probability`
+
+TensorFlow Probability is a library for probabilistic reasoning and statistical analysis in TensorFlow.
+
+* [GitHub](https://github.com/tensorflow/probability)
+* [PyPi](https://pypi.org/project/tensorflow-probability)

envs-flake/flake.nix

@@ -11,7 +11,14 @@
     gensqlquery.url = "github:OpenGen/GenSQL.query";
   };
 
-  outputs = inputs@{ self, nixpkgs, flake-parts, opengen, gensqlquery, ... }:
+  outputs =
+    inputs@{
+      nixpkgs,
+      flake-parts,
+      opengen,
+      gensqlquery,
+      ...
+    }:
     flake-parts.lib.mkFlake { inherit inputs; } {
       imports = [
         # To import a flake module
@@ -20,46 +27,37 @@
         # 3. Add here: foo.flakeModule
         inputs.flake-parts.flakeModules.easyOverlay
       ];
-      systems = [ "x86_64-linux" "aarch64-linux" "aarch64-darwin" "x86_64-darwin" ];
-
+      systems = [
+        "x86_64-linux"
+        "aarch64-linux"
+        "aarch64-darwin"
+        "x86_64-darwin"
+      ];
 
       # NOTE: This property is consumed by flake-parts.mkFlake to specify outputs of
       # the flake that are replicated for each supported system. Typically packages,
       # apps, and devshells are per system.
-      perSystem = { config, self', inputs', pkgs, system, ... }:
-      let
-        toolkit = opengen.lib.basicTools pkgs;
-        sppl = opengen.packages.${system}.sppl;
+      perSystem =
+        { pkgs, system, ... }:
+        let
+          toolkit = opengen.lib.basicTools pkgs;
+          sppl = opengen.packages.${system}.sppl;
 
-        ociImgGensqlQuery = pkgs.callPackage ./images/gensql.query {
-          inherit nixpkgs opengen gensqlquery;
-        };
+          ociImgGensqlQuery = pkgs.callPackage ./images/gensql.query { inherit nixpkgs opengen gensqlquery; };
 
-        ociImgLoom = pkgs.callPackage ./images/gensql.loom {
-          inherit nixpkgs opengen;
-        };
+          ociImgLoom = pkgs.callPackage ./images/gensql.loom { inherit nixpkgs opengen; };
 
-        packages = {
-          inherit
-            ociImgGensqlQuery
-            ociImgLoom
-          ;
-        };
-      in {
-        devShells.default = pkgs.mkShell {
-          packages = [] ++ toolkit;
-        };
+          packages = {
+            inherit ociImgGensqlQuery ociImgLoom;
+          };
+        in
+        {
+          devShells.default = pkgs.mkShell { packages = [ ] ++ toolkit; };
 
-        devShells.sppl = pkgs.mkShell {
-          packages
-            = [sppl]
-            ++ sppl.checkInputs
-            ++ toolkit
-          ;
-        };
+          devShells.sppl = pkgs.mkShell { packages = [ sppl ] ++ sppl.checkInputs ++ toolkit; };
 
-        inherit packages;
-      };
+          inherit packages;
+        };
 
       # NOTE: this property is consumed by flake-parts.mkFlake to define fields
       # of the flake that are NOT per system, such as generic `lib` code or other

envs-flake/images/gensql.loom/default.nix

@@ -1,25 +1,33 @@
-{ pkgs,
+{
+  pkgs,
   nixpkgs,
   opengen,
   system,
-}: let
+}:
+let
   # in OCI context, whatever our host platform we want to build same arch but linux
   systemWithLinux = builtins.replaceStrings [ "darwin" ] [ "linux" ] system;
   crossPkgsLinux = nixpkgs.legacyPackages.${systemWithLinux};
   python = crossPkgsLinux.python3;
 
-  base = opengen.packages.${system}.ociImgBase;
+  base = opengen.packages.${system}.baseOCI;
 
   loom = opengen.packages.${systemWithLinux}.loom;
-in pkgs.dockerTools.buildLayeredImage {
+in
+pkgs.dockerTools.buildLayeredImage {
   name = "probcomp/gensql.loom";
   tag = systemWithLinux;
   fromImage = base;
-  contents = [ loom python ];
+  contents = [
+    loom
+    python
+  ];
   config = {
-    Cmd = [ "${python}/bin/python" "-m" "loom.tasks" ];
-    Env = [
-      "LOOM_STORE=/loom/store"
+    Cmd = [
+      "${python}/bin/python"
+      "-m"
+      "loom.tasks"
     ];
+    Env = [ "LOOM_STORE=/loom/store" ];
   };
 }

envs-flake/images/gensql.query/default.nix

@@ -1,16 +1,17 @@
-{ pkgs,
-  nixpkgs,
+{
+  pkgs,
   system,
   opengen,
   gensqlquery,
-}: let
+}:
+let
   # in OCI context, whatever our host platform we want to build same arch but linux
   systemWithLinux = builtins.replaceStrings [ "darwin" ] [ "linux" ] system;
-  crossPkgsLinux = nixpkgs.legacyPackages.${systemWithLinux};
 
-  base = opengen.packages.${system}.ociImgBase;
+  base = opengen.packages.${system}.baseOCI;
   ociBin = gensqlquery.packages.${systemWithLinux}.bin;
-in pkgs.dockerTools.buildImage {
+in
+pkgs.dockerTools.buildImage {
   name = "probcomp/gensql.query";
   tag = systemWithLinux;
   fromImage = base;