From 06a4011a5695ab8a02e11a40068cfec19cfdff3d Mon Sep 17 00:00:00 2001
From: kjurdzinski <74978240+kjurdzinski@users.noreply.github.com>
Date: Wed, 30 Oct 2024 14:11:18 +0100
Subject: [PATCH 1/6] Remove escher and gseapy, add version of seaborn

---
 environment.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index f406fc0..242bb55 100644
--- a/environment.yml
+++ b/environment.yml
@@ -15,7 +15,7 @@ dependencies:
   - pandas
   - numpy
   - scipy
-  - seaborn
+  - seaborn==0.13.2
   - matplotlib
   - ipywidgets
   # Lab 2
@@ -25,6 +25,4 @@ dependencies:
   - pytest-benchmark
   - pip:
     - cobra
-    - escher
-    - gseapy
     - markupsafe==2.0.1

From 70130c4a5c11b835a53523f706f439d73317a4ca Mon Sep 17 00:00:00 2001
From: kjurdzinski <74978240+kjurdzinski@users.noreply.github.com>
Date: Wed, 30 Oct 2024 14:12:02 +0100
Subject: [PATCH 2/6] Remove escher and gseapy

---
 lab/Lab0/Lab0.ipynb | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/lab/Lab0/Lab0.ipynb b/lab/Lab0/Lab0.ipynb
index 32969e5..a540d9d 100644
--- a/lab/Lab0/Lab0.ipynb
+++ b/lab/Lab0/Lab0.ipynb
@@ -21,14 +21,12 @@
     "\n",
     "from ipywidgets import interact, interact_manual, IntSlider, FloatSlider, Dropdown, Text\n",
     "\n",
-    "import gseapy as gp\n",
     "import sklearn as skl\n",
     "\n",
     "import networkx\n",
     "import statsmodels\n",
     "\n",
-    "import cobra\n",
-    "import escher"
+    "import cobra"
    ]
   },
   {

From 9d70ec16a3221f6d003f11341e5a74b80ab9e714 Mon Sep 17 00:00:00 2001
From: kjurdzinski <74978240+kjurdzinski@users.noreply.github.com>
Date: Wed, 30 Oct 2024 14:17:58 +0100
Subject: [PATCH 3/6] Re-add escher

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index 242bb55..dc06dbe 100644
--- a/environment.yml
+++ b/environment.yml
@@ -23,6 +23,7 @@ dependencies:
   # Lab 3
   - pytest
   - pytest-benchmark
+  - escher
   - pip:
     - cobra
     - markupsafe==2.0.1

From 1ab55563559baa7418cc7631b3e95b1cddbadc35 Mon Sep 17 00:00:00 2001
From: kjurdzinski <74978240+kjurdzinski@users.noreply.github.com>
Date: Wed, 30 Oct 2024 14:18:47 +0100
Subject: [PATCH 4/6] Re-add escher

---
 lab/Lab0/Lab0.ipynb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lab/Lab0/Lab0.ipynb b/lab/Lab0/Lab0.ipynb
index a540d9d..a319373 100644
--- a/lab/Lab0/Lab0.ipynb
+++ b/lab/Lab0/Lab0.ipynb
@@ -26,7 +26,8 @@
     "import networkx\n",
     "import statsmodels\n",
     "\n",
-    "import cobra"
+    "import cobra\n",
+    "import escher"
    ]
   },
   {

From 2553c1dc60dfd8bf55f848270cb3e9427becbfad Mon Sep 17 00:00:00 2001
From: kjurdzinski <74978240+kjurdzinski@users.noreply.github.com>
Date: Wed, 30 Oct 2024 14:27:15 +0100
Subject: [PATCH 5/6] Move escher to pip

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index dc06dbe..f2a6add 100644
--- a/environment.yml
+++ b/environment.yml
@@ -23,7 +23,7 @@ dependencies:
   # Lab 3
   - pytest
   - pytest-benchmark
-  - escher
   - pip:
+    - escher
     - cobra
     - markupsafe==2.0.1

From 8ba736435e56457ef00b33271a5890d4ba7e4052 Mon Sep 17 00:00:00 2001
From: kjurdzinski <74978240+kjurdzinski@users.noreply.github.com>
Date: Wed, 30 Oct 2024 14:46:22 +0100
Subject: [PATCH 6/6] Update cb2030-labs-environment.yml as environment.yml in
 the main folder

---
 lab/Lab0/cb2030-labs-environment.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/lab/Lab0/cb2030-labs-environment.yml b/lab/Lab0/cb2030-labs-environment.yml
index ca371f9..6176f62 100644
--- a/lab/Lab0/cb2030-labs-environment.yml
+++ b/lab/Lab0/cb2030-labs-environment.yml
@@ -15,7 +15,7 @@ dependencies:
   - pandas
   - numpy
   - scipy
-  - seaborn
+  - seaborn==0.13.2
   - matplotlib
   - ipywidgets
   # Lab 2
@@ -24,7 +24,6 @@ dependencies:
   - pytest
   - pytest-benchmark
   - pip:
-    - cobra
     - escher
-    - gseapy
+    - cobra
     - markupsafe==2.0.1