diff --git a/.github/container/Dockerfile.base b/.github/container/Dockerfile.base
index 6857d4267..023576cb5 100644
--- a/.github/container/Dockerfile.base
+++ b/.github/container/Dockerfile.base
@@ -205,7 +205,7 @@ COPY check-shm.sh /opt/nvidia/entrypoint.d/
 
 ADD nsys-jax nsys-jax-combine /usr/local/bin/
 ADD jax_nsys/ /opt/jax_nsys
-ADD requirements-nsys-jax.in /opt/pip-tools.d/
+RUN echo "-e /opt/jax_nsys/python/jax_nsys" > /opt/pip-tools.d/requirements-nsys-jax.in
 RUN ln -s /opt/jax_nsys/install-protoc /usr/local/bin/
 
 ###############################################################################
diff --git a/.github/container/jax_nsys/python/jax_nsys/pyproject.toml b/.github/container/jax_nsys/python/jax_nsys/pyproject.toml
index cc3f3981a..4c5ca9600 100644
--- a/.github/container/jax_nsys/python/jax_nsys/pyproject.toml
+++ b/.github/container/jax_nsys/python/jax_nsys/pyproject.toml
@@ -5,6 +5,9 @@ dependencies = [
   "ipython",
   "numpy",
   "pandas",
+  "protobuf", # a compatible version of protoc needs to be installed out-of-band
   "pyarrow",
+  "requests", # for install-protoc
+  "uncertainties", # communication analysis recipe
 ]
 requires-python = ">= 3.10"
diff --git a/.github/container/jax_nsys/python/jax_nsys_analysis/communication.py b/.github/container/jax_nsys/python/jax_nsys_analysis/communication.py
index 8953b6413..ef02f5c1b 100644
--- a/.github/container/jax_nsys/python/jax_nsys_analysis/communication.py
+++ b/.github/container/jax_nsys/python/jax_nsys_analysis/communication.py
@@ -83,7 +83,8 @@ def format_bandwidth(data, collective):
             return "-" * width
         return f"{data[collective]:>{width}S}"
 
-    for message_size, data in summary_data.items():
+    for message_size in sorted(summary_data.keys()):
+        data = summary_data[message_size]
         print(
             " | ".join(
                 [format_message_size(message_size)]
diff --git a/.github/container/nsys-jax b/.github/container/nsys-jax
index 16d10d82d..104732306 100755
--- a/.github/container/nsys-jax
+++ b/.github/container/nsys-jax
@@ -16,7 +16,6 @@ import subprocess
 import sys
 import tempfile
 import time
-import virtualenv  # type: ignore
 import zipfile
 
 
@@ -544,18 +543,6 @@ def execute_analysis_scripts(mirror_dir, analysis_scripts):
         return [], 0
 
     assert mirror_dir is not None
-    venv_dir = osp.join(mirror_dir, "venv")
-    virtualenv.cli_run([venv_dir, "--python", sys.executable, "--system-site-packages"])
-    subprocess.run(
-        [
-            osp.join(venv_dir, "bin", "pip"),
-            "--disable-pip-version-check",
-            "install",
-            "-e",
-            osp.join(mirror_dir, "python", "jax_nsys"),
-        ],
-        check=True,
-    )
     output = []
     exit_code = 0
     used_slugs = set()
@@ -574,7 +561,7 @@ def execute_analysis_scripts(mirror_dir, analysis_scripts):
         candidates = list(filter(osp.exists, search))
         assert len(candidates), f"Could not find analysis script, tried {search}"
         args.append(mirror_dir)
-        analysis_command = [osp.join(venv_dir, "bin", "python"), candidates[0]] + args
+        analysis_command = [sys.executable, candidates[0]] + args
         # Derive a unique name slug from the analysis script name
         slug = osp.basename(candidates[0]).removesuffix(".py")
         n, suffix = 1, ""
diff --git a/.github/container/nsys-jax-combine b/.github/container/nsys-jax-combine
index c196f9aa3..00e53efb6 100755
--- a/.github/container/nsys-jax-combine
+++ b/.github/container/nsys-jax-combine
@@ -9,7 +9,6 @@ import shutil
 import subprocess
 import sys
 import tempfile
-import virtualenv  # type: ignore
 import zipfile
 
 parser = argparse.ArgumentParser(
@@ -159,20 +158,6 @@ with zipfile.ZipFile(args.output, "w") as ofile:
                         write(dst_info)
     if len(args.analysis):
         assert mirror_dir is not None
-        venv_dir = mirror_dir / "venv"
-        virtualenv.cli_run(
-            [str(venv_dir), "--python", sys.executable, "--system-site-packages"]
-        )
-        subprocess.run(
-            [
-                venv_dir / "bin" / "pip",
-                "--disable-pip-version-check",
-                "install",
-                "-e",
-                mirror_dir / "python" / "jax_nsys",
-            ],
-            check=True,
-        )
         used_slugs = set()
         for analysis in args.analysis:
             # Execute post-processing recipes and add any outputs to `ofile`
@@ -185,9 +170,7 @@ with zipfile.ZipFile(args.output, "w") as ofile:
             candidates = list(filter(lambda p: p.exists(), search))
             assert len(candidates), f"Could not find analysis script, tried {search}"
             analysis_command = (
-                [venv_dir / "bin" / "python", candidates[0]]
-                + script_args
-                + [mirror_dir]
+                [sys.executable, candidates[0]] + script_args + [mirror_dir]
             )
             # Derive a unique name slug from the analysis script name
             slug = os.path.basename(candidates[0]).removesuffix(".py")
@@ -210,7 +193,7 @@ with zipfile.ZipFile(args.output, "w") as ofile:
             # Gather output files of the scrpt
             for path in working_dir.rglob("*"):
                 with open(working_dir / path, "rb") as src, ofile.open(
-                    str(pathlib.Path("analysis") / slug / path), "w"
+                    str(path.relative_to(mirror_dir)), "w"
                 ) as dst:
                     # https://github.com/python/mypy/issues/15031 ?
                     shutil.copyfileobj(src, dst)  # type: ignore
diff --git a/.github/container/pip-finalize.sh b/.github/container/pip-finalize.sh
index 4828af35e..1149d7638 100755
--- a/.github/container/pip-finalize.sh
+++ b/.github/container/pip-finalize.sh
@@ -51,6 +51,6 @@ pip-sync --pip-args '--no-deps --src /opt' requirements.txt
 
 rm -rf ~/.cache/*
 
-# protobuf will be installed at least due to requirements-nsys-jax.in in the base
+# protobuf will be installed at least as a dependency of jax_nsys in the base
 # image, but the installed version is likely to be influenced by other packages.
 install-protoc /usr/local
diff --git a/.github/container/requirements-nsys-jax.in b/.github/container/requirements-nsys-jax.in
deleted file mode 100644
index d07e170f2..000000000
--- a/.github/container/requirements-nsys-jax.in
+++ /dev/null
@@ -1,7 +0,0 @@
-# No version constraint; a compatible version of protoc will be installed later
-protobuf
-# Used by install-protoc
-requests
-virtualenv
-# Used by communication analysis recipe
-uncertainties
diff --git a/.github/workflows/nsys-jax.yaml b/.github/workflows/nsys-jax.yaml
index 4f9f48098..aa91f870c 100644
--- a/.github/workflows/nsys-jax.yaml
+++ b/.github/workflows/nsys-jax.yaml
@@ -38,20 +38,11 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: '3.10'
-      - name: "Create virtual environment"
-        run: |
-          pip install virtualenv
-          virtualenv venv
-      - name: "Install google.protobuf and protoc"
-        run: |
-          ./venv/bin/pip install -r ./JAX-Toolbox/.github/container/requirements-nsys-jax.in
-          ./venv/bin/python ./JAX-Toolbox/.github/container/jax_nsys/install-protoc ./venv
-      - name: "Install jax_nsys Python package"
-        run: ./venv/bin/pip install -e JAX-Toolbox/.github/container/jax_nsys/python/jax_nsys
-      - name: "Install mypy"
-        run: ./venv/bin/pip install matplotlib mypy nbconvert types-protobuf
-      - name: "Install JAX for type-checking, this is a CPU-only build of the latest release"
-        run: ./venv/bin/pip install jax
+      # jax is just a CPU-only build of the latest release for type-checking purposes
+      - name: "Install jax / jax_nsys / mypy"
+        run: pip install jax -e JAX-Toolbox/.github/container/jax_nsys/python/jax_nsys matplotlib mypy nbconvert types-protobuf
+      - name: "Install protoc"
+        run: ./JAX-Toolbox/.github/container/jax_nsys/install-protoc local_protoc
       - name: "Fetch XLA .proto files"
         uses: actions/checkout@v4
         with:
@@ -66,19 +57,19 @@ jobs:
           mkdir compiled_protos compiled_stubs protos
           mv -v xla/third_party/tsl/tsl protos/
           mv -v xla/xla protos/
-          ./venv/bin/python -c "from jax_nsys import compile_protos; compile_protos(proto_dir='protos', output_dir='compiled_protos', output_stub_dir='compiled_stubs')"
+          PATH=${PWD}/local_protoc/bin:$PATH python -c "from jax_nsys import compile_protos; compile_protos(proto_dir='protos', output_dir='compiled_protos', output_stub_dir='compiled_stubs')"
           touch compiled_stubs/py.typed
       - name: "Convert .ipynb to .py"
         shell: bash -x -e {0}
         run: |
           for notebook in $(find ${NSYS_JAX_PYTHON_FILES} -name '*.ipynb'); do
-            ./venv/bin/jupyter nbconvert --to script ${notebook}
+            jupyter nbconvert --to script ${notebook}
           done
       - name: "Run mypy checks"
         shell: bash -x -e {0}
         run: |
           export MYPYPATH="${PWD}/compiled_stubs"
-          ./venv/bin/mypy --scripts-are-modules ${NSYS_JAX_PYTHON_FILES}
+          mypy --scripts-are-modules ${NSYS_JAX_PYTHON_FILES}
 
   # Test nsys-jax-combine and notebook execution; in future perhaps upload the rendered
   # notebook from here too. These input files were generated with something like
@@ -96,24 +87,38 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: '3.12'
+      # TODO: a modern nsys-jax-combine with old .zip input should probably produce a
+      # .zip with a modern jax_nsys/
+      - name: Add modern jax_nsys/ files to static .zip inputs
+        run: |
+          cd .github/container/jax_nsys
+          for zip in ../../workflows/nsys-jax/test_data/pax_fsdp4_4proc_proc*.zip; do
+            zip -ur "${zip}" .
+            zipinfo "${zip}"
+          done
       - name: Use nsys-jax-combine to merge profiles from multiple nsys processes
         shell: bash -x -e {0}
         run: |
-          pip install virtualenv
-          .github/container/nsys-jax-combine \
+          pip install -e .github/container/jax_nsys/python/jax_nsys
+          python .github/container/jax_nsys/install-protoc local_protoc
+          PATH=${PWD}/local_protoc/bin:$PATH .github/container/nsys-jax-combine \
             --analysis summary \
             --analysis communication \
-            -o .github/workflows/nsys-jax/test_data/pax_fsdp4_4proc.zip \
+            -o pax_fsdp4_4proc.zip \
             .github/workflows/nsys-jax/test_data/pax_fsdp4_4proc_proc*.zip
-      - name: Mock up the structure of an extracted .zip file
-        run: unzip -d .github/container/jax_nsys/ .github/workflows/nsys-jax/test_data/pax_fsdp4_4proc.zip
+      - name: Extract the output .zip file
+        run: |
+          mkdir combined/
+          unzip -d combined/ pax_fsdp4_4proc.zip
       - name: Run the install script, but skip launching Jupyter Lab
         shell: bash -x -e {0}
-        run: NSYS_JAX_INSTALL_SKIP_LAUNCH=1 ./.github/container/jax_nsys/install.sh
+        run: |
+          pip install virtualenv
+          NSYS_JAX_INSTALL_SKIP_LAUNCH=1 ./combined/install.sh
       - name: Test the Jupyter Lab installation and execute the notebook
         shell: bash -x -e {0}
         run: |
-          pushd .github/container/jax_nsys
+          pushd combined/
           ./nsys_jax_venv/bin/python -m jupyterlab --version
           # Run with ipython for the sake of getting a clear error message
           ./nsys_jax_venv/bin/ipython Analysis.ipynb