diff --git a/spack-environment/packages.yaml b/spack-environment/packages.yaml
index 7626bd60936d3a5be6eefeafe743ead34d0d62ff..e026404b41886c759bd93a015c33207cde29aaa3 100644
--- a/spack-environment/packages.yaml
+++ b/spack-environment/packages.yaml
@@ -227,7 +227,7 @@ packages:
     - '@2.1.1'
   py-bokeh:
     require:
-    - '@2.4.3'
+    - '@3.3.1'
   py-boto3:
     require:
     - '@1.26.26'
@@ -272,7 +272,7 @@ packages:
     - '@1.16-33-g3788bb4'
   py-numpy:
     require:
-    - '@1.23.4'
+    - '@1.26.1'
   py-pandas:
     require:
     - '@1.5.3'
@@ -282,6 +282,9 @@ packages:
   py-pre-commit:
     require:
     - '@2.20.0'
+  py-pygithub:
+    require:
+    - '@2.1.1'
   py-pycairo:
     require:
     - '@1.20.0'
@@ -290,7 +293,7 @@ packages:
     - '@6.0'
   py-scipy:
     require:
-    - '@1.10.1'
+    - '@1.11.3'
   py-seaborn:
     require:
     - '@0.12.2'
diff --git a/spack.sh b/spack.sh
index 411c680550d9bf858fce116d029d242afebbcaf6..0474d8df8679d5c0014b9606d50d2800f49e0639 100644
--- a/spack.sh
+++ b/spack.sh
@@ -18,6 +18,8 @@ c485709f625429a88a184a099373d76c9438f8e3
 f01774f1d41781bc4b9e5abb5469e234168da663
 cfa2f19f48699a762af77ece8a9c5bc4db3a75d5
 2433f503b73bb515b2e1a7615ae01fea59d2290e
+16f4c53cd4cfb4bc6c9390f6e65217fc9ccc58c9
+d171f314c77ba61b3cd780f159afe6abced5707d
 ---
 ## Ref: https://github.com/spack/spack/commit/[hash]
 ## [hash]: [description]
@@ -31,3 +33,5 @@ cfa2f19f48699a762af77ece8a9c5bc4db3a75d5
 ## f01774f1d41781bc4b9e5abb5469e234168da663: hepmc3: fix from_variant -> self.define
 ## cfa2f19f48699a762af77ece8a9c5bc4db3a75d5: py-htgettoken: use os.environ, avoid AttributeError
 ## 2433f503b73bb515b2e1a7615ae01fea59d2290e: py-htgettoken: allow for undefined variables
+## 16f4c53cd4cfb4bc6c9390f6e65217fc9ccc58c9: py-bokeh: new version 3.3.1, and supporting packages
+## d171f314c77ba61b3cd780f159afe6abced5707d: py-pygithub: new versions, dependencies