Merge pull request #7 from SomaLogic/CAN-18

We are deploying `Canopy` to PyPI as `SomaData` This will make the package easier to install and it will enable users to employ SomaData (f.k.a Canopy) as a dependency in their own packages.

LICENSE

@@ -1,15 +1,15 @@
 # Released under MIT License
 
-Canopy™
+SomaData™
 
-Copyright © 2023 SomaLogic Operating Company, Inc.
+Copyright © 2024 Standard BioTools.
 
-Permission is hereby granted, free of charge, to any person obtaining a copy of the Canopy software
+Permission is hereby granted, free of charge, to any person obtaining a copy of the SomaData software
 and associated documentation files (the "Software"), to deal in the Software without restriction,
 including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense,
 and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions outlined below.  Further, Canopy and SomaLogic are trademarks
-owned by SomaLogic Operating Company, Inc.  No license is hereby granted to these trademarks other than for purposes of
+subject to the following conditions outlined below.  Further, SomaData and SomaLogic are trademarks
+owned by Standard BioTools.  No license is hereby granted to these trademarks other than for purposes of
 identifying the origin or source of the Software.
 
 The above copyright notice and this permission notice shall be included in all copies or substantial

README.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# The Python `Canopy` Package from Somalogic, Inc.\n",
+    "# The Python `SomaData` Package from Somalogic, Inc.\n",
     "\n",
     "![cover](https://img.shields.io/badge/coverage-97-success.svg?style=flat&logo=codecov)\n",
     "[![License:\n",
@@ -14,7 +14,7 @@
     "\n",
     "## Overview\n",
     "\n",
-    "This document accompanies the Python package `canopy`, which loads the SomaLogic, Inc. structured text data file called an `*.adat`.  The `canopy.Adat` object is an extension of the `pandas.DataFrame` class. The package provides auxiliary functions for extracting relevant information from the ADAT object once in the Python environment. Basic familiarity with the Python environment is assumed, as is the ability to install contributed packages from the Python Package Installer (pip)\n",
+    "This document accompanies the Python package `somadata`, which loads the SomaLogic, Inc. structured text data file called an `*.adat`.  The `somadata.Adat` object is an extension of the `pandas.DataFrame` class. The package provides auxiliary functions for extracting relevant information from the ADAT object once in the Python environment. Basic familiarity with the Python environment is assumed, as is the ability to install contributed packages from the Python Package Installer (pip)\n",
     "\n",
     "-----"
    ]
@@ -44,23 +44,32 @@
     "<a name=\"installation\"></a>\n",
     "\n",
     "## Installation\n",
-    "The easiest way to install `Canopy` is to install directly from\n",
+    "\n",
+    "The easiest way to install `SomaData` is to install directly from PyPI\n",
+    "\n",
+    "PIP:\n",
+    "\n",
+    "```bash\n",
+    "pip install SomaData\n",
+    "```\n",
+    "\n",
+    "\n",
     "GitHub:\n",
     "\n",
     "``` bash\n",
-    "pip install git+https://github.com/SomaLogic/canopy.git#egg=canopy\n",
+    "pip install git+https://github.com/SomaLogic/Canopy.git#egg=somadata\n",
     "```\n",
     "\n",
     "Alternatively, if you wish to develop or change the source code, you may clone the repository and install manually via:\n",
     "\n",
     "``` bash\n",
-    "git clone https://github.com/SomaLogic/canopy.git\n",
-    "pip install -e ./canopy\n",
+    "git clone https://github.com/SomaLogic/Canopy.git\n",
+    "pip install -e ./somadata\n",
     "```\n",
     "\n",
     "### Dependencies\n",
     "\n",
-    "`Python >=3.8` is required to install `canopy`. The following package dependencies are installed on a `pip install`:\n",
+    "`Python >=3.8` is required to install `somadata`. The following package dependencies are installed on a `pip install`:\n",
     "  - `pandas >= 1.1.0`\n",
     "  - `numpy >= 1.19.1`\n",
     "\n",
@@ -75,7 +84,7 @@
     "\n",
     "## Basics\n",
     "\n",
-    "Upon installation, load `canopy` as normal:\n",
+    "Upon installation, load `somadata` as normal:\n",
     "\n",
     "[return to top](#toptoc)"
    ]
@@ -86,7 +95,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import canopy"
+    "import somadata"
    ]
   },
   {
@@ -107,10 +116,10 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Help on package canopy:\n",
+      "Help on package somadata:\n",
       "\n",
       "NAME\n",
-      "    canopy\n",
+      "    somadata\n",
       "\n",
       "PACKAGE CONTENTS\n",
       "    adat\n",
@@ -122,15 +131,15 @@
       "    tools (package)\n",
       "\n",
       "FILE\n",
-      "    /Users/tjohnson/code/repos/Canopy/canopy/__init__.py\n",
+      "    /Users/tjohnson/code/repos/SomaData/somadata/__init__.py\n",
       "\n",
       "\n"
      ]
     }
    ],
    "source": [
-    "help(canopy)\n",
-    "# help(canopy.adat) ... etc"
+    "help(somadata)\n",
+    "# help(somadata.adat) ... etc"
    ]
   },
   {
@@ -139,9 +148,9 @@
    "source": [
     "### Internal Objects\n",
     "\n",
-    "The `canopy` package comes with one internal object available to users to run canned examples (or analyses). It can be accessed by perform the import:\n",
+    "The `somadata` package comes with one internal object available to users to run canned examples (or analyses). It can be accessed by perform the import:\n",
     "\n",
-    "  - `from canopy.data.example_data import example_data`"
+    "  - `from somadata.data.example_data import example_data`"
    ]
   },
   {
@@ -175,7 +184,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Loading the sample file from within the canopy library via its path"
+    "Loading the sample file from within the somadata library via its path"
    ]
   },
   {
@@ -186,7 +195,7 @@
     {
      "data": {
       "text/plain": [
-       "canopy.adat.Adat"
+       "somadata.adat.Adat"
       ]
      },
      "execution_count": 3,
@@ -195,7 +204,7 @@
     }
    ],
    "source": [
-    "adat = canopy.read_adat('./canopy/data/example_data.adat')\n",
+    "adat = somadata.read_adat('./somadata/data/example_data.adat')\n",
     "type(adat)"
    ]
   },
@@ -1445,7 +1454,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Canopy's Adat object inherits the pandas printing methods which displays nicely in Jupyter Notebooks when using `IPython.display.display()`."
+    "SomaData's Adat object inherits the pandas printing methods which displays nicely in Jupyter Notebooks when using `IPython.display.display()`."
    ]
   },
   {
@@ -2698,7 +2707,7 @@
     "\n",
     "### Subsetting/Slicing the Dataframe\n",
     "\n",
-    "You may extract certain subgroups of samples and/or features. Canopy augments the pandas dataframe with a number of helper functions to aid the user.\n",
+    "You may extract certain subgroups of samples and/or features. SomaData augments the pandas dataframe with a number of helper functions to aid the user.\n",
     "\n",
     "[return to top](#toptoc)"
    ]
@@ -7698,7 +7707,7 @@
    ],
    "source": [
     "# Observing the Lin's CCC of the lifting scale factors.\n",
-    "from canopy.data import getSomaScanLiftCCC\n",
+    "from somadata.data import getSomaScanLiftCCC\n",
     "\n",
     "# the method returns a pandas dataframe containing the available lift Lins's CCC values:\n",
     "ccc = getSomaScanLiftCCC()\n",
@@ -7778,7 +7787,7 @@
     "<a name=\"example\"></a>\n",
     "\n",
     "# Typical Analyses\n",
-    "Although it is beyond the scope of the `Canopy` package, below are 3\n",
+    "Although it is beyond the scope of the `SomaData` package, below are 3\n",
     "sample analyses that typical users/clients would perform on SomaLogic data.\n",
     "They are not intended to be a definitive guide in statistical\n",
     "analysis and existing packages do exist in the `Python` universe that perform parts\n",
@@ -7805,7 +7814,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from canopy.data.example_data import example_data # Example ADAT included with Canopy\n",
+    "from somadata.data.example_data import example_data # Example ADAT included with SomaData\n",
     "from scipy.stats import ttest_ind\n",
     "from collections import Counter\n",
     "import matplotlib.pyplot as plt\n",

README.md

@@ -1,4 +1,4 @@
-# The Python `Canopy` Package from Somalogic, Inc.
+# The Python `SomaData` Package from Somalogic, Inc.
 
 ![cover](https://img.shields.io/badge/coverage-97-success.svg?style=flat&logo=codecov)
 [![License:
@@ -8,7 +8,7 @@ MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://choosealicense.
 
 ## Overview
 
-This document accompanies the Python package `canopy`, which loads the SomaLogic, Inc. structured text data file called an `*.adat`.  The `canopy.Adat` object is an extension of the `pandas.DataFrame` class. The package provides auxiliary functions for extracting relevant information from the ADAT object once in the Python environment. Basic familiarity with the Python environment is assumed, as is the ability to install contributed packages from the Python Package Installer (pip)
+This document accompanies the Python package `somadata`, which loads the SomaLogic, Inc. structured text data file called an `*.adat`.  The `somadata.Adat` object is an extension of the `pandas.DataFrame` class. The package provides auxiliary functions for extracting relevant information from the ADAT object once in the Python environment. Basic familiarity with the Python environment is assumed, as is the ability to install contributed packages from the Python Package Installer (pip)
 
 -----
 
@@ -28,23 +28,32 @@ This document accompanies the Python package `canopy`, which loads the SomaLogic
 <a name="installation"></a>
 
 ## Installation
-The easiest way to install `Canopy` is to install directly from
+The easiest way to install `SomaData` is to install directly from PyPI
+
+PIP:
+
+```bash
+pip install SomaData
+```
+
+Alternatively one can install from the GitHub repository.
+
 GitHub:
 
 ``` bash
-pip install git+https://github.com/SomaLogic/canopy.git#egg=canopy
+pip install git+https://github.com/SomaLogic/Canopy.git#egg=somadata
 ```
 
 Alternatively, if you wish to develop or change the source code, you may clone the repository and install manually via:
 
 ``` bash
-git clone https://github.com/SomaLogic/canopy.git
-pip install -e ./canopy
+git clone https://github.com/SomaLogic/Canopy.git
+pip install -e ./somadata
 ```
 
 ### Dependencies
 
-`Python >=3.8` is required to install `canopy`. The following package dependencies are installed on a `pip install`:
+`Python >=3.8` is required to install `somadata`. The following package dependencies are installed on a `pip install`:
   - `pandas >= 1.1.0`
   - `numpy >= 1.19.1`
 
@@ -54,27 +63,27 @@ pip install -e ./canopy
 
 ## Basics
 
-Upon installation, load `canopy` as normal:
+Upon installation, load `somadata` as normal:
 
 [return to top](#toptoc)
 
 
 ```python
-import canopy
+import somadata
 ```
 
 ### For a traversable index of the library:
 
 
 ```python
-help(canopy)
-# help(canopy.adat) ... etc
+help(somadata)
+# help(somadata.adat) ... etc
 ```
 
-    Help on package canopy:
+    Help on package somadata:
 
     NAME
-        canopy
+        somadata
 
     PACKAGE CONTENTS
         adat
@@ -86,16 +95,16 @@ help(canopy)
         tools (package)
 
     FILE
-        /Users/tjohnson/code/repos/Canopy/canopy/__init__.py
+        /Users/tjohnson/code/repos/SomaData/somadata/__init__.py
 
 
 
 
 ### Internal Objects
 
-The `canopy` package comes with one internal object available to users to run canned examples (or analyses). It can be accessed by perform the import:
+The `somadata` package comes with one internal object available to users to run canned examples (or analyses). It can be accessed by perform the import:
 
-  - `from canopy.data.example_data import example_data`
+  - `from somadata.data.example_data import example_data`
 
 ## Main Features (I/O)
 
@@ -114,18 +123,18 @@ The `canopy` package comes with one internal object available to users to run ca
 
 [return to top](#toptoc)
 
-Loading the sample file from within the canopy library via its path
+Loading the sample file from within the somadata library via its path
 
 
 ```python
-adat = canopy.read_adat('./canopy/data/example_data.adat')
+adat = somadata.read_adat('./somadata/data/example_data.adat')
 type(adat)
 ```
 
 
 
 
-    canopy.adat.Adat
+    somadata.adat.Adat
 
 
 
@@ -1331,7 +1340,7 @@ adat.header_metadata
 
 
 
-Canopy's Adat object inherits the pandas printing methods which displays nicely in Jupyter Notebooks when using `IPython.display.display()`.
+SomaData's Adat object inherits the pandas printing methods which displays nicely in Jupyter Notebooks when using `IPython.display.display()`.
 
 <a name="wrangling"></a>
 
@@ -2368,7 +2377,7 @@ sqrt_adat = adat.apply(np.sqrt)  # equivlane to `np.sqrt(adat)`
 
 ### Subsetting/Slicing the Dataframe
 
-You may extract certain subgroups of samples and/or features. Canopy augments the pandas dataframe with a number of helper functions to aid the user.
+You may extract certain subgroups of samples and/or features. SomaData augments the pandas dataframe with a number of helper functions to aid the user.
 
 [return to top](#toptoc)
 
@@ -5920,7 +5929,7 @@ lifted_adat = adat.lift('11K')
 
 ```python
 # Observing the Lin's CCC of the lifting scale factors.
-from canopy.data import getSomaScanLiftCCC
+from somadata.data import getSomaScanLiftCCC
 
 # the method returns a pandas dataframe containing the available lift Lins's CCC values:
 ccc = getSomaScanLiftCCC()
@@ -6111,7 +6120,7 @@ adat.to_adat('/tmp/out_file.adat')
 <a name="example"></a>
 
 # Typical Analyses
-Although it is beyond the scope of the `Canopy` package, below are 3
+Although it is beyond the scope of the `SomaData` package, below are 3
 sample analyses that typical users/clients would perform on SomaLogic data.
 They are not intended to be a definitive guide in statistical
 analysis and existing packages do exist in the `Python` universe that perform parts
@@ -6128,7 +6137,7 @@ preliminary analyses on SomaLogic data for:
 
 
 ```python
-from canopy.data.example_data import example_data # Example ADAT included with Canopy
+from somadata.data.example_data import example_data # Example ADAT included with SomaData
 from scipy.stats import ttest_ind
 from collections import Counter
 import matplotlib.pyplot as plt

bin/canopy_check_adat → bin/somadata_check_adat

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 import argparse
-from canopy import Adat
+from somadata import Adat
 
 
 if __name__ == '__main__':
@@ -27,4 +27,4 @@ if __name__ == '__main__':
             print('SUCCESS')
         except Exception as e:
             print('FAILURE')
-            print('Adat read error, please send the adat to Joey or Ted for debugging with the following error message: ' + str(e))
+            print('Adat read error, please contact support@somalogic.com for debugging with the ADAT file and following error message: ' + str(e))