release v0.1.2 (#167)

* release v0.1.2
pinellolab · Apr 16, 2023 · d556dc2 · d556dc2
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diff --git a/conda/colab/construct.yaml b/conda/colab/construct.yaml
@@ -1,5 +1,5 @@
 name: pyrovelocity-colab
-version: 0.1.1
+version: 0.1.2
 
 channels:
   - conda-forge

diff --git a/docs/history.md b/docs/history.md
@@ -1,5 +1,9 @@
 # History
 
+## 0.1.2 (2023-04-16)
+
+- See [0.1.2](https://github.com/pinellolab/pyrovelocity/releases/tag/v0.1.2)
+
 ## 0.1.1 (2023-02-16)
 
 - See [0.1.1](https://github.com/pinellolab/pyrovelocity/releases/tag/v0.1.1)

diff --git a/docs/source/notebooks/pyrovelocity_colab_template.ipynb b/docs/source/notebooks/pyrovelocity_colab_template.ipynb
@@ -1,71 +1,55 @@
 {
-  "nbformat": 4,
-  "nbformat_minor": 0,
-  "metadata": {
-    "colab": {
-      "provenance": []
-    },
-    "kernelspec": {
-      "name": "python3",
-      "display_name": "Python 3"
-    },
-    "language_info": {
-      "name": "python"
-    },
-    "accelerator": "GPU",
-    "gpuClass": "standard"
-  },
   "cells": [
     {
       "cell_type": "markdown",
-      "source": [
-        "# Pyrovelocity Colab notebook template"
-      ],
       "metadata": {
         "id": "Qpk2p3N13W_Q"
-      }
+      },
+      "source": [
+        "# Pyrovelocity Colab notebook template"
+      ]
     },
     {
       "cell_type": "markdown",
-      "source": [
-        "## Setup environment"
-      ],
       "metadata": {
         "id": "9r9zVJED3bfH"
-      }
+      },
+      "source": [
+        "## Setup environment"
+      ]
     },
     {
       "cell_type": "markdown",
-      "source": [
-        "### Install conda environment"
-      ],
       "metadata": {
         "id": "tnQdC9wi3dpY"
-      }
+      },
+      "source": [
+        "### Install conda environment"
+      ]
     },
     {
       "cell_type": "markdown",
-      "source": [
-        "This first stage will download and install the environment. It takes about 5 minutes. The runtime will then automatically restart. Skip execution of this cell after the restart."
-      ],
       "metadata": {
         "id": "eylffLqA3GVb"
-      }
+      },
+      "source": [
+        "This first stage will download and install the environment. It takes about 5 minutes. The runtime will then automatically restart. Skip execution of this cell after the restart."
+      ]
     },
     {
       "cell_type": "code",
       "execution_count": null,
       "metadata": {
-        "id": "K4YU4y6VX4qR",
         "colab": {
           "base_uri": "https://localhost:8080/"
         },
+        "id": "K4YU4y6VX4qR",
         "outputId": "392f66ec-c2ed-4ba5-94f6-a4fdd884e242"
       },
       "outputs": [
         {
-          "output_type": "stream",
           "name": "stdout",
+          "output_type": "stream",
           "text": [
             "⏬ Downloading https://storage.googleapis.com/pyrovelocity/data/scripts/pyrovelocity-colab-0.1.1-Linux-x86_64.sh...\n",
             "📦 Installing...\n",
@@ -77,7 +61,7 @@
         }
       ],
       "source": [
-        "pyrovelocity_version = \"0.1.1\"\n",
+        "pyrovelocity_version = \"0.1.2\"\n",
         "pyrovelocity_colab_script_url = \\\n",
         "\"https://storage.googleapis.com/pyrovelocity/data/scripts/\" + \\\n",
         "f\"pyrovelocity-colab-{pyrovelocity_version}-Linux-x86_64.sh\"\n",
@@ -91,91 +75,107 @@
     },
     {
       "cell_type": "markdown",
-      "source": [
-        "### Install library"
-      ],
       "metadata": {
         "id": "sKUW7Jyq3hMc"
-      }
+      },
+      "source": [
+        "### Install library"
+      ]
     },
     {
       "cell_type": "markdown",
-      "source": [
-        "You can install the upstream or a fork development version by appropriately editing the `git clone` url."
-      ],
       "metadata": {
         "id": "zWZpJCqQ3jcs"
-      }
+      },
+      "source": [
+        "You can install the upstream or a fork development version by appropriately editing the `git clone` url."
+      ]
     },
     {
       "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "lOPLeXosRx9M"
+      },
+      "outputs": [],
       "source": [
         "%cd /content\n",
         "%rm -f \"__installer__.sh\"\n",
         "!git clone https://github.com/pinellolab/pyrovelocity.git"
-      ],
-      "metadata": {
-        "id": "lOPLeXosRx9M"
-      },
-      "execution_count": null,
-      "outputs": []
+      ]
     },
     {
       "cell_type": "markdown",
-      "source": [
-        "Because google colab uses python 3.9, you may need to edit the python version constraint in `pyproject.toml` to install in colab."
-      ],
       "metadata": {
         "id": "v_lKa94u4g2Z"
-      }
+      },
+      "source": [
+        "Because google colab uses python 3.9, you may need to edit the python version constraint in `pyproject.toml` to install in colab."
+      ]
     },
     {
       "cell_type": "code",
+      "execution_count": null,
+      "metadata": {
+        "id": "dnBcNhqk4fxa"
+      },
+      "outputs": [],
       "source": [
         "!pip install --user --no-deps -e pyrovelocity\n",
         "from IPython import get_ipython\n",
         "get_ipython().kernel.do_shutdown(True)"
-      ],
-      "metadata": {
-        "id": "dnBcNhqk4fxa"
-      },
-      "execution_count": null,
-      "outputs": []
+      ]
     },
     {
       "cell_type": "markdown",
-      "source": [
-        "If this is successful, the following commands should print the location of the `__init__.py` file for the pyrovelocity package and the currently installed version."
-      ],
       "metadata": {
         "id": "kk76Hz3g3_FR"
-      }
+      },
+      "source": [
+        "If this is successful, the following commands should print the location of the `__init__.py` file for the pyrovelocity package and the currently installed version."
+      ]
     },
     {
       "cell_type": "code",
-      "source": [
-        "import pyrovelocity\n",
-        "print(pyrovelocity.__file__)\n",
-        "print(pyrovelocity.__version__)"
-      ],
+      "execution_count": null,
       "metadata": {
         "colab": {
           "base_uri": "https://localhost:8080/"
         },
         "id": "QvXoFzK-zATP",
         "outputId": "f2a47888-6fc6-47c5-d3df-631173840ae2"
       },
-      "execution_count": null,
       "outputs": [
         {
-          "output_type": "stream",
           "name": "stdout",
+          "output_type": "stream",
           "text": [
             "/content/pyrovelocity/pyrovelocity/__init__.py\n",
             "0.1.1\n"
           ]
         }
+      ],
+      "source": [
+        "import pyrovelocity\n",
+        "print(pyrovelocity.__file__)\n",
+        "print(pyrovelocity.__version__)"
       ]
     }
-  ]
+  ],
+  "metadata": {
+    "accelerator": "GPU",
+    "colab": {
+      "provenance": []
+    },
+    "gpuClass": "standard",
+    "kernelspec": {
+      "display_name": "Python 3",
+      "name": "python3"
+    },
+    "language_info": {
+      "name": "python"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 0
 }
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyrovelocity"
-version = "0.1.1"
+version = "0.1.2"
 description = "A multivariate RNA Velocity model to estimate future cell states with uncertainty using probabilistic modeling with pyro."
 authors = ["Qian Qin <[email protected]>"]
 license = "AGPL-3.0-only"
@@ -11,7 +11,7 @@ documentation = "https://pyrovelocity.readthedocs.io"
 classifiers = [
   "Development Status :: 2 - Pre-Alpha",
   "Intended Audience :: Developers",
-  "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+  "License :: OSI Approved :: GNU Affero General Public License v3",
   "Natural Language :: English",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3.9",
@@ -143,36 +143,6 @@ dev = [
 # optional = true
 
 # [tool.poetry.group.dev.dependencies]
-# Pygments = ">=2.10.0"
-# black = ">=21.10b0"
-# coverage = {extras = ["toml"], version = ">=6.2"}
-# darglint = ">=1.8.1"
-# flake8 = ">=4.0.1"
-# flake8-bandit = ">=2.1.2"
-# flake8-bugbear = ">=21.9.2"
-# flake8-docstrings = ">=1.6.0"
-# flake8-rst-docstrings = ">=0.2.5"
-# furo = ">=2021.11.12"
-# isort = ">=5.10.1"
-# mypy = ">=0.930"
-# pep8-naming = ">=0.12.1"
-# pre-commit = ">=2.16.0"
-# pre-commit-hooks = ">=4.1.0"
-# pytest = ">=6.2.5"
-# pyupgrade = ">=2.29.1"
-# safety = ">=1.10.3"
-# sphinx = ">=4.3.2"
-# sphinx-autobuild = ">=2021.3.14"
-# sphinx-click = ">=3.0.2"
-# typeguard = ">=2.13.3"
-# xdoctest = {extras = ["colors"], version = ">=0.15.10"}
-# myst-parser = {version = ">=0.16.1"}
-# dparse = ">=0.5.2"
-# pytest-cov = "^4.0.0"
-# pytest-mock = "^3.10.0"
-# poethepoet = "^0.16.0"
-# dvc-gs = "^2.20.0"
-# jupyter-core = "^5.1.3"
 
 [tool.poetry.scripts]
 pyrovelocity = "pyrovelocity.pyrovelocity:main"
@@ -183,7 +153,7 @@ pyrovelocity = "pyrovelocity.pyrovelocity:main"
 # $ poetry install
 # $ poetry run poe force-cuda11
 [tool.poe.tasks]
-force-cuda11 = "python -m pip install torch==1.8.1+cu111 --extra-index-url https://download.pytorch.org/whl/cu111"
+force-cuda11 = "python -m pip install torch==1.13.1+cu111 --extra-index-url https://download.pytorch.org/whl/cu111"
 
 [tool.coverage.paths]
 source = ["src", "*/site-packages"]
@@ -214,27 +184,3 @@ ignore_missing_imports = true
 [build-system]
 requires = ["poetry-core>=1.1.0"]
 build-backend = "poetry.core.masonry.api"
-
-# plan to upgrade torch installation to tool.poetry.source
-# not yet functioning smoothly in poetry 1.2.2
-# e.g. https://github.com/python-poetry/poetry/issues/4885
-#      https://github.com/python-poetry/poetry/issues/2613
-#      "https://discuss.python.org/t/what-to-do-about-gpus-
-#      and-the-built-distributions-that-support-them/7125"
-# docs: https://python-poetry.org/docs/repositories/#package-sources
-# will require
-# torch = { version = "1.8.1+cu111", source = "torch" }
-# in tool.poetry.dependencies
-# instead of
-# torch = [
-#   { url = "https://download.pytorch.org/whl/cu111/torch-1.8.1%2Bcu111-cp38-cp38-linux_x86_64.whl", markers = "sys_platform == 'linux'" },
-#   { url = "https://download.pytorch.org/whl/cu111/torch-1.8.1%2Bcu111-cp38-cp38-win_amd64.whl", markers = "sys_platform == 'win32'" },
-#   { version = "1.8.1", markers = "sys_platform == 'darwin'" }
-# ]
-#
-# [[tool.poetry.source]]
-# name = "torch"
-# url = "https://download.pytorch.org/whl/torch_stable.html"
-# url = "https://download.pytorch.org/whl/cu111/"
-# default = false
-# secondary = false