From c95015ad770848c4a2efed38bbcab73c08f8d26d Mon Sep 17 00:00:00 2001
From: Alex Dowling <alex@dowlinglab.org>
Date: Mon, 9 Mar 2026 10:02:45 -0400
Subject: [PATCH 1/2] Update installation.rst

Fixed filename error in instructions
---
 doc/online_docs/installation.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/online_docs/installation.rst b/doc/online_docs/installation.rst
index fdb5b6e..0aefe47 100644
--- a/doc/online_docs/installation.rst
+++ b/doc/online_docs/installation.rst
@@ -25,7 +25,7 @@ Installation
 
 For installation, we recommend the use of conda environments to control packages dependencies and PharmaPy. A lighweight version of conda (`miniconda`_) is probably a good option for new users of the management system.
 
-For PharmaPy installation, you must use the source code, which is available in our `Github repository`_. Once the source code is downloaded to the desired location, navigate (:code:`cd`) to the directory which contains the setup.py file. Then, follow the instructions on the :code:`installation_guide.txt`, to setup fresh conda environment and install PharmaPy and its dependencies.
+For PharmaPy installation, you must use the source code, which is available in our `Github repository`_. Once the source code is downloaded to the desired location, navigate (:code:`cd`) to the directory which contains the setup.py file. Then, follow the instructions on the :code:`instal_instructions.txt`, to setup fresh conda environment and install PharmaPy and its dependencies.
 
 ..
         make sure your conda environment is appropriately installed and activated, then input the following commands for PharmaPy installation:

From 26b6d0971df922eb5588a1432121941518fc06ec Mon Sep 17 00:00:00 2001
From: Alex Dowling <adowling@nd.edu>
Date: Mon, 9 Mar 2026 10:20:48 -0400
Subject: [PATCH 2/2] Updated (outdated/confusing) installation instructions

---
 .gitignore               | 34 +++++++++++++++++++++++-----------
 install_instructions.txt | 26 ++++++++++++++++----------
 setup.py                 | 19 +++++++++----------
 3 files changed, 48 insertions(+), 31 deletions(-)

diff --git a/.gitignore b/.gitignore
index 25af2e3..bfab791 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,9 +7,12 @@ target/
 # Jupyter Notebook
 .ipynb_checkpoints
 
-# pyenv
-*.python-version
-*.pyc
+# pyenv
+*.python-version
+*.pyc
+__pycache__/
+*.pyo
+*.pyd
 
 # celery beat schedule file
 celerybeat-schedule
@@ -17,10 +20,12 @@ celerybeat-schedule
 # dotenv
 .env
 
-# virtualenv
-.venv/
-venv/
-ENV/
+# virtualenv
+.venv/
+venv/
+ENV/
+.conda/
+conda-meta/
 
 # Spyder project settings
 .spyderproject
@@ -76,9 +81,16 @@ ENV/
 *.ppt
 *.pptx
 
-# Compressed files
-*.zip
-*.tar.gz
-*.rar
+# Compressed files
+*.zip
+*.tar.gz
+*.rar
+
+# Packaging artifacts
+*.egg-info/
+*.eggs/
+build/
+dist/
+pip-wheel-metadata/
 
 source/crystallization/
diff --git a/install_instructions.txt b/install_instructions.txt
index cfc2ceb..02705a0 100644
--- a/install_instructions.txt
+++ b/install_instructions.txt
@@ -16,7 +16,9 @@ Step 4: After this step, both PharmaPy dependencies and PharmaPy itself should b
 
 Step 5: Activate the new environment by doing: conda activate <name_of_environment> (exclude <>)
 
-Step 6: Test PharmaPy by moving to the tests/ directory (cd tests) and then running: python reactor_tests.py
+Step 6: Test PharmaPy by moving to the integration test directory and running:
+	cd tests/integration
+	python reactor_tests.py
 
 # ---------- Manual installation ----------
 Step 1: Create a conda environment named <env_name> (optional)
@@ -47,15 +49,19 @@ conda config -- show envs_dirs
 step 1.1.2: Create a path
 conda create --prefix <Directory address + /<env_name>>
 
-Step 2: Install the package requirements in requirements.txt
-
-conda install -c conda-forge --file requirements.txt
-
-Step 3: Install PharmaPy; navigate to the source directory
-
-python setup.py develop
-
-Step 4: Check to see if the package is working by running a test in tests/
+Step 2: Install the package requirements in requirements.txt
+
+conda install -c conda-forge --file requirements.txt -y
+
+Step 3: Install PharmaPy; navigate to the source directory
+
+pip install -e .
+
+Step 4: Check to see if the package is working
+
+python -c "import PharmaPy; print('PharmaPy import OK')"
+cd tests/integration
+python reactor_tests.py
 
 
 
diff --git a/setup.py b/setup.py
index 9eceef7..592e637 100644
--- a/setup.py
+++ b/setup.py
@@ -1,15 +1,14 @@
-from setuptools import setup, find_packages, Extension
+from setuptools import setup, find_packages
 
 # Read the content of requirements.txt into a list
 with open("requirements.txt", "r") as f:
     requirements = f.read().splitlines()
 
-setup(name='PharmaPy',
-      version='0.0.1',
-      packages=find_packages(),
-      author='Daniel Casas-Orozco',
-      author_email='dcasasor@purdue.edu',
-      license='',
-      url='',
-      py_modules=["PharmaPy"],
-      install_requires=requirements)
\ No newline at end of file
+setup(name='PharmaPy',
+      version='0.0.1',
+      packages=find_packages(),
+      author='Daniel Casas-Orozco',
+      author_email='dcasasor@purdue.edu',
+      license='',
+      url='',
+      install_requires=requirements)