diff --git a/requirements-dev.txt b/requirements-dev.txt
index b9f3efc2..047125eb 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -13,4 +13,3 @@ pytest-cov==4.1.0
 python-dateutil==2.8.2
 ruff==0.1.3
 tox==4.11.3
-numpy==2.0.0
diff --git a/requirements-doc.txt b/requirements-doc.txt
index 3f80ea45..4b921319 100644
--- a/requirements-doc.txt
+++ b/requirements-doc.txt
@@ -1,2 +1,6 @@
 # dependencies to generate the documentation for HDMF-Zarr
-
+matplotlib
+sphinx>=4  # improved support for docutils>=0.17
+sphinx_rtd_theme>=1  # <1 does not work with docutils>=0.17
+sphinx-gallery
+sphinx-copybutton
diff --git a/requirements-opt.txt b/requirements-opt.txt
index 771f5d04..6fc3bcb0 100644
--- a/requirements-opt.txt
+++ b/requirements-opt.txt
@@ -1,3 +1,3 @@
-tqdm==4.66.4
-fsspec==2024.6.0
-s3fs==2024.6.0
+tqdm==4.67.0
+fsspec==2024.10.0
+s3fs==2024.10.0
diff --git a/requirements.txt b/requirements.txt
index 6b7cb6aa..840b4815 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,7 +1,7 @@
 # pinned dependencies to reproduce an entire development environment to use HDMF-ZARR
-hdmf==3.14.3
-zarr==2.16.1
-pynwb==2.5.0
-numpy==2.0.0
-numcodecs==0.12.1
-threadpoolctl==3.2.0
+hdmf==3.14.5
+zarr==2.18.3
+pynwb==2.8.2
+numpy==2.1.3
+numcodecs==0.13.1
+threadpoolctl==3.5.0