From 414f85dcf92f96f750b835fc4a9a4ff003bd32e3 Mon Sep 17 00:00:00 2001
From: Mehdi Seifi <mehdiseifi@gmail.com>
Date: Mon, 17 Nov 2025 10:45:45 +0100
Subject: [PATCH 1/4] updated numpy version; added dependabot.yml

---
 .github/dependabot.yml | 10 ++++++++++
 pyproject.toml         |  8 ++++++--
 2 files changed, 16 insertions(+), 2 deletions(-)
 create mode 100644 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..b8316f4
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    # Files stored in repository root
+    directory: "/"
+    schedule:
+      interval: "daily"
+      time: "08:00"
+    ignore:
+      - dependency-name: "torchmetrics"
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 90c5343..fd784fc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ name = "microssim"
 dynamic = ["version"]
 description = "Improved structural similarity metrics for comparing microscopy data."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.11"
 license = { text = "BSD-3-Clause" }
 authors = [
     { name = 'Ashesh' },
@@ -37,12 +37,16 @@ classifiers = [
     "Typing :: Typed",
 ]
 dependencies = [
-    "numpy<2",
+    "numpy>=1.21",
     "scipy",
     "scikit-image",
     "torch",
     "torchmetrics",
     "tqdm",
+    "jupyterlab>=4.4.10",
+    "pooch>=1.8.2",
+    "matplotlib>=3.10.7",
+    "seaborn>=0.13.2",
 ]
 
 [project.optional-dependencies]

From 377eeb64fe381ddc8d4dc9b1e925fb401be60c79 Mon Sep 17 00:00:00 2001
From: Mehdi Seifi <mehdiseifi@gmail.com>
Date: Mon, 17 Nov 2025 10:55:28 +0100
Subject: [PATCH 2/4] drop example notebook dependencies

---
 pyproject.toml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index fd784fc..01dff26 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,10 +43,6 @@ dependencies = [
     "torch",
     "torchmetrics",
     "tqdm",
-    "jupyterlab>=4.4.10",
-    "pooch>=1.8.2",
-    "matplotlib>=3.10.7",
-    "seaborn>=0.13.2",
 ]
 
 [project.optional-dependencies]

From 757f47c34bec8280cde2cfdbc72832f6ea867bd1 Mon Sep 17 00:00:00 2001
From: Mehdi Seifi <mehdiseifi@gmail.com>
Date: Mon, 17 Nov 2025 11:01:37 +0100
Subject: [PATCH 3/4] updated ci for python >=3.11

---
 .github/workflows/ci.yml       | 2 +-
 .github/workflows/coverage.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5ca71b8..e786fed 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12"]
         # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
         platform: [ubuntu-latest, macos-13, windows-latest]
 
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index a04f6bd..a24652e 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
         platform: [ubuntu-latest]
 
     steps:

From 9013aff1a27cff081668ba73c80d262ab7c2ab29 Mon Sep 17 00:00:00 2001
From: Mehdi Seifi <mehdiseifi@gmail.com>
Date: Wed, 19 Nov 2025 11:48:27 +0100
Subject: [PATCH 4/4] pinned upper version for dependencies

---
 .github/dependabot.yml |  2 +-
 pyproject.toml         | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index b8316f4..f891ab7 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -7,4 +7,4 @@ updates:
       interval: "daily"
       time: "08:00"
     ignore:
-      - dependency-name: "torchmetrics"
\ No newline at end of file
+      - dependency-name: "torchmetrics"
diff --git a/pyproject.toml b/pyproject.toml
index 01dff26..2925fe1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,12 +37,12 @@ classifiers = [
     "Typing :: Typed",
 ]
 dependencies = [
-    "numpy>=1.21",
-    "scipy",
-    "scikit-image",
-    "torch",
-    "torchmetrics",
-    "tqdm",
+    "numpy>=1.21,<3.0.0",
+    "scipy<=1.16.3",
+    "scikit-image<=0.25.2",
+    "torch<=2.9.1",
+    "torchmetrics<=1.8.2",
+    "tqdm<=4.67.1",
 ]
 
 [project.optional-dependencies]