rectanglepy 0.0.45__tar.gz → 0.1.2__tar.gz

{rectanglepy-0.0.45 → rectanglepy-0.1.2}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.45
+current_version = 0.1.2
 tag = True
 commit = True
 

rectanglepy-0.1.2/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,21 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+    - type: markdown
+      attributes:
+          value: |
+              **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+              detailing how to provide the necessary information for us to reproduce your bug. In brief:
+                * Please provide exact steps how to reproduce the bug in a clean Python environment.
+                * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+                * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+                  available datasets or to share a subset of your data.
+
+    - type: textarea
+      id: report
+      attributes:
+          label: Report
+          description: A clear and concise description of what the bug is.
+      validations:
+          required: true

{rectanglepy-0.0.45 → rectanglepy-0.1.2}/CHANGELOG.md

@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning][].
 
 ## [Unreleased]
 
+## [0.1.0] - 2024-04-25
+
 ### Added
 
--   Basic tool, preprocessing and plotting functions
+-   Initial public release of Rectangle.

{rectanglepy-0.0.45 → rectanglepy-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: rectanglepy
-Version: 0.0.45
+Version: 0.1.2
 Summary: Hierarchical deconvolution of bulk  transcriptomics
 Project-URL: Documentation, https://rectanglepy.readthedocs.io/
 Project-URL: Source, https://github.com/ComputationalBiomedicineGroup/Rectangle
@@ -55,9 +55,9 @@ Description-Content-Type: text/markdown
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
 
-[badge-tests]: https://img.shields.io/github/actions/workflow/status/bernheder/Rectangle/test.yaml?branch=main
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/ComputationalBiomedicineGroup/Rectangle/build.yaml?branch=main
 [link-tests]: https://github.com/ComputationalBiomedicineGroup/Rectangle/actions/workflows/build.yaml
-[badge-docs]: https://img.shields.io/readthedocs/Rectangle
+[badge-docs]: https://img.shields.io/readthedocs/rectanglepy
 
 Rectangle embodies a ”second-generation” deconvolution methodology, setting itself apart from other second-generation
 methods through its efficiency in signature creation and its handling of challenges within the deconvolution process.
@@ -97,6 +97,6 @@ If you found a bug, please use the [issue tracker][issue-tracker].
 
 [scverse-discourse]: https://discourse.scverse.org/
 [issue-tracker]: https://github.com/ComputationalBiomedicineGroup/Rectangle/issues
-[changelog]: https://Rectanglepy.readthedocs.io/latest/changelog.html
+[changelog]: https://rectanglepy.readthedocs.io/changelog.html
 [link-docs]: https://Rectanglepy.readthedocs.io
 [link-api]: https://rectanglepy.readthedocs.io/api.html

{rectanglepy-0.0.45 → rectanglepy-0.1.2}/README.md

@@ -3,9 +3,9 @@
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
 
-[badge-tests]: https://img.shields.io/github/actions/workflow/status/bernheder/Rectangle/test.yaml?branch=main
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/ComputationalBiomedicineGroup/Rectangle/build.yaml?branch=main
 [link-tests]: https://github.com/ComputationalBiomedicineGroup/Rectangle/actions/workflows/build.yaml
-[badge-docs]: https://img.shields.io/readthedocs/Rectangle
+[badge-docs]: https://img.shields.io/readthedocs/rectanglepy
 
 Rectangle embodies a ”second-generation” deconvolution methodology, setting itself apart from other second-generation
 methods through its efficiency in signature creation and its handling of challenges within the deconvolution process.
@@ -45,6 +45,6 @@ If you found a bug, please use the [issue tracker][issue-tracker].
 
 [scverse-discourse]: https://discourse.scverse.org/
 [issue-tracker]: https://github.com/ComputationalBiomedicineGroup/Rectangle/issues
-[changelog]: https://Rectanglepy.readthedocs.io/latest/changelog.html
+[changelog]: https://rectanglepy.readthedocs.io/changelog.html
 [link-docs]: https://Rectanglepy.readthedocs.io
 [link-api]: https://rectanglepy.readthedocs.io/api.html

{rectanglepy-0.0.45 → rectanglepy-0.1.2}/docs/conf.py

@@ -34,7 +34,7 @@ needs_sphinx = "4.0"
 html_context = {
     "display_github": True,  # Integrate GitHub
     "github_user": "ComputationalBiomedicineGroup",  # Username
-    "github_repo": "rectangle",  # Repo name
+    "github_repo": "Rectangle",  # Repo name
     "github_version": "main",  # Version
     "conf_py_path": "/docs/",  # Path in the checkout to the docs root
 }

rectanglepy-0.1.2/docs/notebooks/example.ipynb

@@ -0,0 +1,351 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Example workflow"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-03-25T16:12:40.629887Z",
+     "start_time": "2024-03-25T16:12:39.074585Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "import rectanglepy as rectangle\n",
+    "from anndata import AnnData"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Load tutorial data"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2024-03-25T16:12:41.282874Z",
+     "start_time": "2024-03-25T16:12:40.630684Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "sc_counts, annotations, bulks  = rectangle.load_tutorial_data()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "                       MIR1302-2HG  AL627309.1  AL627309.4  AC114498.1   \nE2L4_GATGCTACAGGCACAA            0           0           0           0  \\\nL5_AACAACCAGGAACTAT              0           0           0           0   \nL5_TCCTTCTGTACTCCGG              0           0           0           0   \nL2_GCCCGAACACGTATAC              0           0           0           0   \nE2L2_ATGCATGTCACACCCT            0           0           0           0   \n\n                       AL669831.5  FAM41C  AL645608.5  NOC2L  PERM1  ISG15  \nE2L4_GATGCTACAGGCACAA           0       0           0      0      0      7  \nL5_AACAACCAGGAACTAT             0       0           0      0      0      1  \nL5_TCCTTCTGTACTCCGG             0       0           0      0      0      0  \nL2_GCCCGAACACGTATAC             0       0           0      0      0      2  \nE2L2_ATGCATGTCACACCCT           0       1           0      0      0      1  ",
+      "text/html": "<div>\n<style scoped>\n    .dataframe tbody tr th:only-of-type {\n        vertical-align: middle;\n    }\n\n    .dataframe tbody tr th {\n        vertical-align: top;\n    }\n\n    .dataframe thead th {\n        text-align: right;\n    }\n</style>\n<table border=\"1\" class=\"dataframe\">\n  <thead>\n    <tr style=\"text-align: right;\">\n      <th></th>\n      <th>MIR1302-2HG</th>\n      <th>AL627309.1</th>\n      <th>AL627309.4</th>\n      <th>AC114498.1</th>\n      <th>AL669831.5</th>\n      <th>FAM41C</th>\n      <th>AL645608.5</th>\n      <th>NOC2L</th>\n      <th>PERM1</th>\n      <th>ISG15</th>\n    </tr>\n  </thead>\n  <tbody>\n    <tr>\n      <th>E2L4_GATGCTACAGGCACAA</th>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>7</td>\n    </tr>\n    <tr>\n      <th>L5_AACAACCAGGAACTAT</th>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>1</td>\n    </tr>\n    <tr>\n      <th>L5_TCCTTCTGTACTCCGG</th>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n    </tr>\n    <tr>\n      <th>L2_GCCCGAACACGTATAC</th>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>2</td>\n    </tr>\n    <tr>\n      <th>E2L2_ATGCATGTCACACCCT</th>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>1</td>\n      <td>0</td>\n      <td>0</td>\n      <td>0</td>\n      <td>1</td>\n    </tr>\n  </tbody>\n</table>\n</div>"
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "sc_counts.iloc[:, :10].head()"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-25T16:12:41.300170Z",
+     "start_time": "2024-03-25T16:12:41.284686Z"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "E2L4_GATGCTACAGGCACAA    Monocytes\nL5_AACAACCAGGAACTAT      Monocytes\nL5_TCCTTCTGTACTCCGG      Monocytes\nL2_GCCCGAACACGTATAC      Monocytes\nE2L2_ATGCATGTCACACCCT    Monocytes\nName: 0, dtype: object"
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "annotations.head()"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-25T16:12:41.982618Z",
+     "start_time": "2024-03-25T16:12:41.979126Z"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "         UBE2Q2P2  SSX9   CXorf67   EFCAB8  SPATA31B1P  SDR16C6P     GTPBP6   \npbmc_1   0.000000   0.0  0.118865  0.00000         0.0       0.0  57.280197  \\\npbmc_10  0.081115   0.0  0.086782  0.00000         0.0       0.0  72.275326   \npbmc_12  0.000000   0.0  0.188464  0.03157         0.0       0.0  50.997427   \n\n          EFCAB12       A1BG  A1CF  \npbmc_1   0.252188  10.863071   0.0  \npbmc_10  0.095742  14.785649   0.0  \npbmc_12  0.100608   7.492537   0.0  ",
+      "text/html": "<div>\n<style scoped>\n    .dataframe tbody tr th:only-of-type {\n        vertical-align: middle;\n    }\n\n    .dataframe tbody tr th {\n        vertical-align: top;\n    }\n\n    .dataframe thead th {\n        text-align: right;\n    }\n</style>\n<table border=\"1\" class=\"dataframe\">\n  <thead>\n    <tr style=\"text-align: right;\">\n      <th></th>\n      <th>UBE2Q2P2</th>\n      <th>SSX9</th>\n      <th>CXorf67</th>\n      <th>EFCAB8</th>\n      <th>SPATA31B1P</th>\n      <th>SDR16C6P</th>\n      <th>GTPBP6</th>\n      <th>EFCAB12</th>\n      <th>A1BG</th>\n      <th>A1CF</th>\n    </tr>\n  </thead>\n  <tbody>\n    <tr>\n      <th>pbmc_1</th>\n      <td>0.000000</td>\n      <td>0.0</td>\n      <td>0.118865</td>\n      <td>0.00000</td>\n      <td>0.0</td>\n      <td>0.0</td>\n      <td>57.280197</td>\n      <td>0.252188</td>\n      <td>10.863071</td>\n      <td>0.0</td>\n    </tr>\n    <tr>\n      <th>pbmc_10</th>\n      <td>0.081115</td>\n      <td>0.0</td>\n      <td>0.086782</td>\n      <td>0.00000</td>\n      <td>0.0</td>\n      <td>0.0</td>\n      <td>72.275326</td>\n      <td>0.095742</td>\n      <td>14.785649</td>\n      <td>0.0</td>\n    </tr>\n    <tr>\n      <th>pbmc_12</th>\n      <td>0.000000</td>\n      <td>0.0</td>\n      <td>0.188464</td>\n      <td>0.03157</td>\n      <td>0.0</td>\n      <td>0.0</td>\n      <td>50.997427</td>\n      <td>0.100608</td>\n      <td>7.492537</td>\n      <td>0.0</td>\n    </tr>\n  </tbody>\n</table>\n</div>"
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "bulks.iloc[:, :10].head()"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-25T16:12:43.131140Z",
+     "start_time": "2024-03-25T16:12:43.127235Z"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Convert to AnnData object"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "outputs": [],
+   "source": [
+    "sc_adata = AnnData(sc_counts, obs=annotations.to_frame(name=\"cell_type\"))"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-25T16:15:38.118620Z",
+     "start_time": "2024-03-25T16:15:38.098633Z"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Single step Rectangle workflow"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "estimations, signature_result = rectangle.rectangle(sc_adata, bulks)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "code",
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "          B cells       ILC  Monocytes  NK cells  Plasma cells  Platelet   \npbmc_1   0.075919  0.001291   0.279064  0.046658      0.010834  0.008950  \\\npbmc_10  0.093986  0.003410   0.316445  0.033528      0.002279  0.036153   \npbmc_12  0.060533  0.017572   0.251589  0.114043      0.002038  0.027041   \n\n         T cells CD4 conv  T cells CD8     Tregs       mDC       pDC   Unknown  \npbmc_1           0.139600     0.268706  0.069930  0.017415  0.001971  0.079661  \npbmc_10          0.243435     0.146063  0.011599  0.032518  0.005273  0.075309  \npbmc_12          0.119488     0.325029  0.024586  0.027099  0.004422  0.026560  ",
+      "text/html": "<div>\n<style scoped>\n    .dataframe tbody tr th:only-of-type {\n        vertical-align: middle;\n    }\n\n    .dataframe tbody tr th {\n        vertical-align: top;\n    }\n\n    .dataframe thead th {\n        text-align: right;\n    }\n</style>\n<table border=\"1\" class=\"dataframe\">\n  <thead>\n    <tr style=\"text-align: right;\">\n      <th></th>\n      <th>B cells</th>\n      <th>ILC</th>\n      <th>Monocytes</th>\n      <th>NK cells</th>\n      <th>Plasma cells</th>\n      <th>Platelet</th>\n      <th>T cells CD4 conv</th>\n      <th>T cells CD8</th>\n      <th>Tregs</th>\n      <th>mDC</th>\n      <th>pDC</th>\n      <th>Unknown</th>\n    </tr>\n  </thead>\n  <tbody>\n    <tr>\n      <th>pbmc_1</th>\n      <td>0.075919</td>\n      <td>0.001291</td>\n      <td>0.279064</td>\n      <td>0.046658</td>\n      <td>0.010834</td>\n      <td>0.008950</td>\n      <td>0.139600</td>\n      <td>0.268706</td>\n      <td>0.069930</td>\n      <td>0.017415</td>\n      <td>0.001971</td>\n      <td>0.079661</td>\n    </tr>\n    <tr>\n      <th>pbmc_10</th>\n      <td>0.093986</td>\n      <td>0.003410</td>\n      <td>0.316445</td>\n      <td>0.033528</td>\n      <td>0.002279</td>\n      <td>0.036153</td>\n      <td>0.243435</td>\n      <td>0.146063</td>\n      <td>0.011599</td>\n      <td>0.032518</td>\n      <td>0.005273</td>\n      <td>0.075309</td>\n    </tr>\n    <tr>\n      <th>pbmc_12</th>\n      <td>0.060533</td>\n      <td>0.017572</td>\n      <td>0.251589</td>\n      <td>0.114043</td>\n      <td>0.002038</td>\n      <td>0.027041</td>\n      <td>0.119488</td>\n      <td>0.325029</td>\n      <td>0.024586</td>\n      <td>0.027099</td>\n      <td>0.004422</td>\n      <td>0.026560</td>\n    </tr>\n  </tbody>\n</table>\n</div>"
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "estimations"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-25T16:18:17.737030Z",
+     "start_time": "2024-03-25T16:18:17.731946Z"
+    }
+   },
+   "execution_count": 9
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "signature_result is a [`RectangleSignatureResult`](../generated/rectanglepy.pp.RectangleSignatureResult.rst) object. Results of estimations vary slightly from machine to machine (due to difference in theunderlying linear algebra packages)"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Even sampling and consensus"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "We recommend even subsampling of the sc data.\n",
+    "You can use the `sample_size` parameter to sample a fixed number of cells per cell type,  and run the consensus multiple times to get a more robust result."
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "estimations, signature_result = rectangle.rectangle(sc_adata, bulks, consensus_runs=5, sample_size=1500)"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# 2-step Rectangle workflow"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "Rectangle can also be run in two steps, first creating the signature and then deconvoluting the bulk data."
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Create Signature result"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "signature_result = rectangle.pp.build_rectangle_signatures(sc_adata, bulks=bulks)"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "This creates a [`RectangleSignatureResult`](../generated/rectanglepy.pp.RectangleSignatureResult.rst) object."
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Deconvolute bulk data"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "estimations = rectangle.tl.deconvolution(signature_result, bulks)"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "This returns a pandas DataFrame with the estimated cell type proportions."
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-03-07T18:39:06.840457Z",
+     "start_time": "2024-03-07T18:39:06.838965Z"
+    }
+   },
+   "execution_count": 21
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3.9.12 ('squidpy39')",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "ae6466e8d4f517858789b5c9e8f0ed238fb8964458a36305fca7bddc149e9c64"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

{rectanglepy-0.0.45 → rectanglepy-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "rectanglepy"
-version = "0.0.45"
+version = "0.1.2"
 description = "Hierarchical deconvolution of bulk  transcriptomics"
 readme = "README.md"
 requires-python = ">=3.10"

{rectanglepy-0.0.45 → rectanglepy-0.1.2}/src/rectanglepy/pp/create_signature.py

@@ -142,8 +142,6 @@ def _run_deseq2(countsig: pd.DataFrame, n_cpus: int = None) -> dict[str | int, p
         clinical_df = pd.DataFrame({"condition": condition}, index=countsig.columns)
         dds = DeseqDataSet(counts=count_df, metadata=clinical_df, design_factors="condition", quiet=True, n_cpus=n_cpus)
         dds.deseq2()
-        dds.varm["LFC"] = dds.varm["LFC"].round(4)
-        dds.varm["dispersions"] = dds.varm["dispersions"].round(3)
 
         stat_res = DeseqStats(dds, n_cpus=n_cpus, quiet=True)
         stat_res.summary(quiet=True)

{rectanglepy-0.0.45 → rectanglepy-0.1.2}/src/rectanglepy/rectangle.py

@@ -105,13 +105,13 @@ def load_tutorial_data() -> tuple[pd.DataFrame, pd.DataFrame, pd.DataFrame]:
     -------
     The single-cell count data, annotations, and bulk data.
     """
-    with resource_stream(__name__, "data/hao1_annotations_small.csv") as annotations_file:
-        annotations = pd.read_csv(annotations_file, index_col=0)["0"]
+    with resource_stream(__name__, "data/hao1_annotations_small.zip") as annotations_file:
+        annotations = pd.read_csv(annotations_file, index_col=0, compression="zip")["0"]
 
-    with resource_stream(__name__, "data/hao1_counts_small.csv") as counts_file:
-        sc_counts = pd.read_csv(counts_file, index_col=0).astype("int")
+    with resource_stream(__name__, "data/hao1_counts_small.zip") as counts_file:
+        sc_counts = pd.read_csv(counts_file, index_col=0, compression="zip").astype("int")
 
-    with resource_stream(__name__, "data/small_fino_bulks.csv") as bulks_file:
-        bulks = pd.read_csv(bulks_file, index_col=0)
+    with resource_stream(__name__, "data/small_fino_bulks.zip") as bulks_file:
+        bulks = pd.read_csv(bulks_file, index_col=0, compression="zip")
 
     return sc_counts.T, annotations, bulks.T

{rectanglepy-0.0.45 → rectanglepy-0.1.2}/tests/test_rectangle.py

@@ -16,7 +16,7 @@ def test_rectangle():
     sc_data, annotations, bulks = rectanglepy.load_tutorial_data()
     sc_data_adata = AnnData(sc_data, obs=annotations.to_frame(name="cell_type"))
 
-    result = rectanglepy.rectangle(sc_data_adata, bulks, optimize_cutoffs=False, p=0.1, lfc=0.5)
+    result = rectanglepy.rectangle(sc_data_adata, bulks)
 
     assert isinstance(result[0], pd.DataFrame)
     assert isinstance(result[1], RectangleSignatureResult)
@@ -27,7 +27,7 @@ def test_rectangle_consensus():
     sc_data_adata = AnnData(sc_data, obs=annotations.to_frame(name="cell_type"))
 
     result = rectanglepy.rectangle(
-        sc_data_adata, bulks, optimize_cutoffs=False, p=0.5, lfc=0.0, consensus_runs=2, sample_size=9
+        sc_data_adata, bulks, optimize_cutoffs=False, p=0.5, lfc=0.0, consensus_runs=2, sample_size=50
     )
 
     assert isinstance(result[0], pd.DataFrame)

rectanglepy-0.0.45/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,89 +0,0 @@
-name: Bug report
-description: Report something that is broken or incorrect
-labels: bug
-body:
-    - type: markdown
-      attributes:
-          value: |
-              **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
-              detailing how to provide the necessary information for us to reproduce your bug. In brief:
-                * Please provide exact steps how to reproduce the bug in a clean Python environment.
-                * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
-                * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
-                  available datasets or to share a subset of your data.
-
-    - type: textarea
-      id: report
-      attributes:
-          label: Report
-          description: A clear and concise description of what the bug is.
-      validations:
-          required: true
-
-    - type: textarea
-      id: versions
-      attributes:
-          label: Version information
-          description: |
-              Please paste below the output of
-
-              ```python
-              import session_info
-              session_info.show(html=False, dependencies=True)
-              ```
-          placeholder: |
-              -----
-              anndata             0.8.0rc2.dev27+ge524389
-              session_info        1.0.0
-              -----
-              asttokens           NA
-              awkward             1.8.0
-              backcall            0.2.0
-              cython_runtime      NA
-              dateutil            2.8.2
-              debugpy             1.6.0
-              decorator           5.1.1
-              entrypoints         0.4
-              executing           0.8.3
-              h5py                3.7.0
-              ipykernel           6.15.0
-              jedi                0.18.1
-              mpl_toolkits        NA
-              natsort             8.1.0
-              numpy               1.22.4
-              packaging           21.3
-              pandas              1.4.2
-              parso               0.8.3
-              pexpect             4.8.0
-              pickleshare         0.7.5
-              pkg_resources       NA
-              prompt_toolkit      3.0.29
-              psutil              5.9.1
-              ptyprocess          0.7.0
-              pure_eval           0.2.2
-              pydev_ipython       NA
-              pydevconsole        NA
-              pydevd              2.8.0
-              pydevd_file_utils   NA
-              pydevd_plugins      NA
-              pydevd_tracing      NA
-              pygments            2.12.0
-              pytz                2022.1
-              scipy               1.8.1
-              setuptools          62.5.0
-              setuptools_scm      NA
-              six                 1.16.0
-              stack_data          0.3.0
-              tornado             6.1
-              traitlets           5.3.0
-              wcwidth             0.2.5
-              zmq                 23.1.0
-              -----
-              IPython             8.4.0
-              jupyter_client      7.3.4
-              jupyter_core        4.10.0
-              -----
-              Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) [GCC 10.3.0]
-              Linux-5.18.6-arch1-1-x86_64-with-glibc2.35
-              -----
-              Session information updated at 2022-07-07 17:55