From dfd2493682628ec44129076664a931e2aa2fd2f6 Mon Sep 17 00:00:00 2001
From: Justin Hiemstra <jhiemstra@wisc.edu>
Date: Fri, 29 Sep 2023 16:24:32 +0000
Subject: [PATCH] Incorporate feedback from code review

In general, this was just implementing @agitter's suggested changes. One of the questions
that was raised was why I unpinned the version of docutils. I had to double check, but it
looks like pinning the version caused a compatibility issue, specifically with the pip-
installed package `sphinx-rtd-theme`. Rather than unpinning Docutils or bumping it down by
a version, I bumped `sphinx-rtd-theme` up two versions (in both `environment.yaml` and
the `pyproject.toml`) to satisfy the dependency conflict. The change appears not to have
caused issues, but I'm also not aware of how the doc-building mechanism works, so I'm
not sure how to give it a more robust test.
---
 environment.yml |  4 ++--
 pyproject.toml  | 22 +++++++++++++---------
 2 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/environment.yml b/environment.yml
index 3d3fb949..75546ef0 100644
--- a/environment.yml
+++ b/environment.yml
@@ -13,7 +13,7 @@ dependencies:
   - python=3.8
   - pip=22.1
   - requests=2.28
-  - scikit-learn=1.1
+  - scikit-learn=1.2
   - seaborn=0.12
   - spython=0.2
   # Only required for GraphSpace
@@ -25,4 +25,4 @@ dependencies:
   - sphinx=5.0
   - pip:
      - graphspace_python==1.3.1
-     - sphinx-rtd-theme==1.0.0
+     - sphinx-rtd-theme==1.2.0
diff --git a/pyproject.toml b/pyproject.toml
index 89aaae1c..5962fc3c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,16 +1,20 @@
 [project]
-name = "SPRAS"
-version = "v0.0.1"
-description = "Signaling Pathway Reconstruction Analysis Streamliner (SPRAS)"
+name = "spras"
+version = "0.0.1"
+description = "Signaling Pathway Reconstruction Analysis Streamliner"
 authors = [
-  { name = "Anthony Gitter", email = "agitter@morgridge.org" },
+  { name = "Anthony Gitter", email = "gitter@biostat.wisc.edu" },
+  { name = "Anna Ritz", email = "aritz@reed.edu"},
 ]
 license = { file = "LICENSE" }
 readme = "README.md"
 classifiers = [
-    "Programming Language :: Python :: 3",
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 requires-python = ">=3.8"
 dependencies = [
@@ -22,18 +26,18 @@ dependencies = [
     "pandas==1.4",
     "pip==22.1",
     "requests==2.28",
-    "scikit-learn==1.2", #Version bumped from 1.1-->1.2 to get past compilation errors. No other errors encountered
+    "scikit-learn==1.2",
     "seaborn==0.12",
     "spython==0.2",
     # Only required for GraphSpace
     "commonmark==0.9",
-    "docutils", #==0.18
+    "docutils==0.18",
     "jinja2==3.1",
     "mock==4.0",
     "recommonmark==0.7",
     "sphinx==5.0",
     "graphspace_python==1.3.1",
-    "sphinx-rtd-theme==1.0.0",
+    "sphinx-rtd-theme==1.2.0",
 ]
 
 [project.optional-dependencies]
@@ -45,7 +49,7 @@ dev = [
 
 [project.urls]
 "Homepage" = "https://github.com/Reed-CompBio/spras"
-"Bug Tracker" = "https://github.com/Reed-CompBio/spras/issues"
+"Issues" = "https://github.com/Reed-CompBio/spras/issues"
 
 [build-system]
 requires = ["setuptools>=64.0"]