Merge pull request #2 from scbirlab/fixes

Fixes
scbirlab · Oct 11, 2024 · fd52979 · fd52979
2 parents ea8ab81 + dcfdcec
commit fd52979
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diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -12,12 +12,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

diff --git a/README.md b/README.md
@@ -8,8 +8,6 @@ Cleaning, collating, and augmenting chemical datasets.
 
 - [Installation](#installation)
 - [Command-line usage](#command-line-usage)
-    - [Example](#example)
-    - [Other commands](#other-commands)
 - [Python API](#python-api)
 - [Documentation](#documentation)
 
@@ -33,30 +31,47 @@ pip install -e .
 
 ## Command-line usage
 
-**schemist**  provides command-line utlities to ... The tools complete specific tasks which 
-can be easily composed into analysis pipelines, because the TSV table output goes to
-`stdout` by default so they can be piped from one tool to another.
-
-To get a list of commands (tools), do
+**schemist**  provides command-line utlities. The list of commands can be checked like so:
 
 ```bash
-schemist --help
+$ schemist --help
+usage: schemist [-h] [--version] {clean,convert,featurize,collate,dedup,enumerate,react,split} ...
+
+Tools for cleaning, collating, and augmenting chemical datasets.
+
+options:
+  -h, --help            show this help message and exit
+  --version, -v         show program's version number and exit
+
+Sub-commands:
+  {clean,convert,featurize,collate,dedup,enumerate,react,split}
+                        Use these commands to specify the tool you want to use.
+    clean               Clean and normalize SMILES column of a table.
+    convert             Convert between string representations of chemical structures.
+    featurize           Convert between string representations of chemical structures.
+    collate             Collect disparate tables or SDF files of libraries into a single table.
+    dedup               Deduplicate chemical structures and retain references.
+    enumerate           Enumerate bio-chemical structures within length and sequence constraints.
+    react               React compounds in silico in indicated columns using a named reaction.
+    split               Split table based on chosen algorithm, optionally taking account of chemical structure during splits.
 ```
 
-And to get help for a specific command, do
+Each command is designed to work on large data files in a streaming fashion, so that the entire file is not held in memory at once. One caveat is that the scaffold-based splits are very slow with tables of millions of rows.
+
+All commands (except `collate`) take from the input table a named column with a SMILES, SELFIES, amino-acid sequence, HELM, or InChI representation of compounds.
+
+The tools complete specific tasks which 
+can be easily composed into analysis pipelines, because the TSV table output goes to
+`stdout` by default so they can be piped from one tool to another.
+
+To get help for a specific command, do
 
 ```bash
 schemist <command> --help
 ```
 
 For the Python API, [see below](#python-api).
 
-## Example
-
-
-## Other commands
-
-
 
 ## Python API
 
@@ -66,8 +81,6 @@ For the Python API, [see below](#python-api).
 >>> import schemist as sch
 ```
 
-
-
 ## Documentation
 
 Full API documentation is at [ReadTheDocs](https://schemist.readthedocs.org).
diff --git a/docs/source/index.md b/docs/source/index.md
@@ -4,7 +4,7 @@
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/schemist)
 ![PyPI](https://img.shields.io/pypi/v/schemist)
 
-Cleaning, collating, and augmenting chemical datasets.
+Organizing and processing tables of chemical structures.
 
 ```{toctree}
 :maxdepth: 2
@@ -16,6 +16,10 @@ python
 modules
 ```
 
+## Issues, problems, suggestions
+
+Add to the [issue tracker](https://www.github.com/schemist/issues).
+
 ## Source
 
-`GitHub <https://github.com/scbirlab/schemist>`_
+View source at [GitHub](https://github.com/scbirlab/schemist).
diff --git a/docs/source/installation.md b/docs/source/installation.md
@@ -0,0 +1,17 @@
+# Installation
+
+## The easy way
+
+Install the pre-compiled version from GitHub:
+
+```bash
+$ pip install schemist
+```
+
+## From source
+
+Clone the [repository](https://www.github.com/schemist), then `cd` into it. Then run:
+
+```bash
+pip install -e .
+```
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
@@ -0,0 +1,7 @@
+schemist
+========
+
+.. toctree::
+   :maxdepth: 4
+
+   schemist
diff --git a/docs/source/schemist.rst b/docs/source/schemist.rst
@@ -0,0 +1,109 @@
+schemist package
+================
+
+Submodules
+----------
+
+schemist.cleaning module
+------------------------
+
+.. automodule:: schemist.cleaning
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.cli module
+-------------------
+
+.. automodule:: schemist.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.collating module
+-------------------------
+
+.. automodule:: schemist.collating
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.converting module
+--------------------------
+
+.. automodule:: schemist.converting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.features module
+------------------------
+
+.. automodule:: schemist.features
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.generating module
+--------------------------
+
+.. automodule:: schemist.generating
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.io module
+------------------
+
+.. automodule:: schemist.io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.rest\_lookup module
+----------------------------
+
+.. automodule:: schemist.rest_lookup
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.splitting module
+-------------------------
+
+.. automodule:: schemist.splitting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.tables module
+----------------------
+
+.. automodule:: schemist.tables
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.typing module
+----------------------
+
+.. automodule:: schemist.typing
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+schemist.utils module
+---------------------
+
+.. automodule:: schemist.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: schemist
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/usage.md b/docs/source/usage.md
@@ -0,0 +1,55 @@
+# Usage
+
+**schemist** has a variety of utilities which can be used through the command-line or the [Python API](#python-api).
+
+## Command-line usage
+
+**schemist**  provides command-line utlities. The list of commands can be checked like so:
+
+```bash
+$ schemist --help
+usage: schemist [-h] [--version] {clean,convert,featurize,collate,dedup,enumerate,react,split} ...
+
+Tools for cleaning, collating, and augmenting chemical datasets.
+
+options:
+  -h, --help            show this help message and exit
+  --version, -v         show program's version number and exit
+
+Sub-commands:
+  {clean,convert,featurize,collate,dedup,enumerate,react,split}
+                        Use these commands to specify the tool you want to use.
+    clean               Clean and normalize SMILES column of a table.
+    convert             Convert between string representations of chemical structures.
+    featurize           Convert between string representations of chemical structures.
+    collate             Collect disparate tables or SDF files of libraries into a single table.
+    dedup               Deduplicate chemical structures and retain references.
+    enumerate           Enumerate bio-chemical structures within length and sequence constraints.
+    react               React compounds in silico in indicated columns using a named reaction.
+    split               Split table based on chosen algorithm, optionally taking account of chemical structure during splits.
+```
+
+Each command is designed to work on large data files in a streaming fashion, so that the entire file is not held in memory at once. One caveat is that the scaffold-based splits are very slow with tables of millions of rows.
+
+All commands (except `collate`) take from the input table a named column with a SMILES, SELFIES, amino-acid sequence, HELM, or InChI representation of compounds.
+
+The tools complete specific tasks which 
+can be easily composed into analysis pipelines, because the TSV table output goes to
+`stdout` by default so they can be piped from one tool to another.
+
+To get help for a specific command, do
+
+```bash
+schemist <command> --help
+```
+
+For the Python API, [see below](#python-api).
+
+
+## Python API
+
+You can access the underlying functions of `schemist` to help custom analyses or develop other tools.
+
+```python
+>>> import schemist as sch
+```
diff --git a/pyproject.toml b/pyproject.toml
@@ -28,15 +28,15 @@ classifiers = [
 ]
 
 dependencies = [ 
-  "carabiner-tools[pd]",
+  "carabiner-tools[pd]>=0.0.3.post1",
   "datamol",
-  "descriptastorus",
+  "descriptastorus==2.6.1",
   "nemony",
   "openpyxl==3.1.0", 
   "pandas",
   "rdkit",
   "requests",
-  "selfies"
+  "selfies",
 ]
 
 [project.urls]