From 82e948f8e3624da1fbecdd48a812e99ad2970a1d Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <45482070+hwpang@users.noreply.github.com>
Date: Sat, 15 Jun 2024 13:40:48 -0400
Subject: [PATCH 1/3] Case sensitive when cd

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 9c9a857..f609a34 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,7 @@ We recommend using [conda](https://docs.conda.io/en/latest/) to install QupKake.
 Clone the repository:
 ```bash
 git clone https://github.com/Shualdon/QupKake.git
-cd qupkake
+cd QupKake
 ```
 
 Create a conda environment from the environment.yml file:
@@ -56,7 +56,7 @@ conda activate qupkake
 Clone the repository and install using pip:
 ```bash
 git clone https://github.com/Shualdon/QupKake.git
-cd qupkake
+cd QupKake
 pip install .
 ```
 This will install the package and all the rest of the dependencies.

From 3a9dc89166bb2dda78b0774cfbb2ec6cc557db62 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <45482070+hwpang@users.noreply.github.com>
Date: Sat, 15 Jun 2024 13:44:07 -0400
Subject: [PATCH 2/3] The environment file extension in the repo is .yaml, not
 .yml

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index f609a34..6bf98e4 100644
--- a/README.md
+++ b/README.md
@@ -33,9 +33,9 @@ git clone https://github.com/Shualdon/QupKake.git
 cd QupKake
 ```
 
-Create a conda environment from the environment.yml file:
+Create a conda environment from the environment.yaml file:
 ```bash
-conda env create -f environment.yml
+conda env create -f environment.yaml
 conda activate qupkake
 ```
 This will create a conda environment with all the dependencies installed.

From cf7f6b922730c2c187815f36f9d2bb26720dd083 Mon Sep 17 00:00:00 2001
From: Hao-Wei Pang <45482070+hwpang@users.noreply.github.com>
Date: Sat, 15 Jun 2024 14:30:00 -0400
Subject: [PATCH 3/3] Update README.md

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 6bf98e4..9db06fa 100644
--- a/README.md
+++ b/README.md
@@ -108,9 +108,9 @@ $ qupkake file <filename>
 
 Specific flags for this input type are:
 ```bash
--s, --smiles_col: column name for SMILES strings. Default: smiles
+-s, --smiles-col: column name for SMILES strings. Default: smiles
 
--n, --name_col: column name for molecule names. Default: name
+-n, --name-col: column name for molecule names. Default: name
 
 -o, --output: output file name (SDF with pKa predictions). Default: qupkake_output.sdf
 ```