Merge pull request #1239 from minrk/3.11

Support Python 3.11 and upgrade jupyterhub from 1.5.0 to 3.1.1

repo2docker/buildpacks/conda/__init__.py

@@ -1,10 +1,12 @@
 """BuildPack for conda environments"""
 import os
 import re
+import warnings
 from collections.abc import Mapping
 
 from ruamel.yaml import YAML
 
+from ...semver import parse_version as V
 from ...utils import is_local_pip_requirement
 from .._r_base import rstudio_base_scripts
 from ..base import BaseImage
@@ -98,7 +100,7 @@ class CondaBuildPack(BaseImage):
         """
         path = super().get_path()
         path.insert(0, "${CONDA_DIR}/bin")
-        if self.py2:
+        if self.separate_kernel_env:
             path.insert(0, "${KERNEL_PYTHON_PREFIX}/bin")
         path.insert(0, "${NB_PYTHON_PREFIX}/bin")
         # This is at the end of $PATH, for backwards compat reasons
@@ -172,20 +174,24 @@ class CondaBuildPack(BaseImage):
         frozen_name = f"environment-{self._conda_platform()}.lock"
         pip_frozen_name = "requirements.txt"
         if py_version:
-            if self.python_version == "2.7":
-                if "linux-64" != self._conda_platform():
+            conda_platform = self._conda_platform()
+            if self.separate_kernel_env:
+                self.log.warning(
+                    f"User-requested packages for legacy Python version {py_version} will be installed in a separate kernel environment.\n"
+                )
+                lockfile_name = f"environment.py-{py_version}-{conda_platform}.lock"
+                if not os.path.exists(os.path.join(HERE, lockfile_name)):
                     raise ValueError(
-                        f"Python version 2.7 {self._conda_platform()} is not supported!"
+                        f"Python version {py_version} on {conda_platform} is not supported!"
                     )
-
-                # python 2 goes in a different env
                 files[
-                    "conda/environment.py-2.7-linux-64.lock"
+                    f"conda/{lockfile_name}"
                 ] = self._kernel_environment_file = "/tmp/env/kernel-environment.lock"
-                # additional pip requirements for kernel env
-                if os.path.exists(os.path.join(HERE, "requirements.py-2.7.txt")):
+
+                requirements_file_name = f"requirements.py-{py_version}.pip"
+                if os.path.exists(os.path.join(HERE, requirements_file_name)):
                     files[
-                        "conda/requirements.py-2.7.txt"
+                        f"conda/{requirements_file_name}"
                     ] = (
                         self._kernel_requirements_file
                     ) = "/tmp/env/kernel-requirements.txt"
@@ -333,8 +339,26 @@ class CondaBuildPack(BaseImage):
     @property
     def py2(self):
         """Am I building a Python 2 kernel environment?"""
+        warnings.warn(
+            "CondaBuildPack.py2 is deprecated in 2023.2. Use CondaBuildPack.separate_kernel_env.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         return self.python_version and self.python_version.split(".")[0] == "2"
 
+    # Python versions _older_ than this get a separate kernel env
+    kernel_env_cutoff_version = "3.7"
+
+    @property
+    def separate_kernel_env(self):
+        """Whether the kernel should be installed into a separate env from the server
+
+        Applies to older versions of Python that aren't kept up-to-date
+        """
+        return self.python_version and V(self.python_version) < V(
+            self.kernel_env_cutoff_version
+        )
+
     def get_preassemble_script_files(self):
         """preassembly only requires environment.yml
 
@@ -352,7 +376,11 @@ class CondaBuildPack(BaseImage):
         """Return series of build-steps specific to this source repository."""
         scripts = []
         environment_yml = self.binder_path("environment.yml")
-        env_prefix = "${KERNEL_PYTHON_PREFIX}" if self.py2 else "${NB_PYTHON_PREFIX}"
+        env_prefix = (
+            "${KERNEL_PYTHON_PREFIX}"
+            if self.separate_kernel_env
+            else "${NB_PYTHON_PREFIX}"
+        )
         if os.path.exists(environment_yml):
             # TODO: when using micromamba, we call $MAMBA_EXE install -p ...
             # whereas mamba/conda need `env update -p ...` when it's an env.yaml file

repo2docker/buildpacks/conda/environment-linux-64.lock

@@ -1,42 +1,34 @@
 # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-01-23 11:59:03 UTC
+# Frozen on 2023-02-03 12:33:27 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 3b780a798011d21422fbbea52f1c94325fc806c944f506d41d0bdf397b93c604
+# input_hash: 56d66ed1f6b5535bd09b3fb8546cc5bdb3cea65aa2ed89ffaf52424a63c739aa
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+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3
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@@ -64,11 +56,10 @@ https://conda.anaconda.org/conda-forge/noarch/pandocfilters-1.5.0-pyhd8ed1ab_0.t
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-https://conda.anaconda.org/conda-forge/noarch/prometheus_client-0.15.0-pyhd8ed1ab_0.tar.bz2#b260ed41427dbbe70537b3030c643b2e
+https://conda.anaconda.org/conda-forge/noarch/prometheus_client-0.16.0-pyhd8ed1ab_0.conda#8efaddc1c8b8ce262c4d1a7c6571c799
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@@ -78,24 +69,24 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f
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+https://conda.anaconda.org/conda-forge/noarch/setuptools-67.1.0-pyhd8ed1ab_0.conda#845dae446df791b5e1a3eaa6454640c1
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repo2docker/buildpacks/conda/environment-linux-aarch64.lock

@@ -1,41 +1,33 @@
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-# Frozen on 2023-01-23 12:00:09 UTC
+# Frozen on 2023-02-03 12:33:35 UTC
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repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock

@@ -1,12 +1,12 @@
 # AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-01-23 12:08:19 UTC
+# Frozen on 2023-02-03 12:34:24 UTC
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repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock

@@ -1,11 +1,11 @@
 # AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY
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+# Frozen on 2023-02-03 12:34:31 UTC
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repo2docker/buildpacks/conda/environment.py-3.10.yml

@@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-01-23 12:08:19 UTC
+# Generated on 2023-02-03 12:34:24 UTC
 channels:
 - conda-forge
 dependencies:
@@ -10,6 +10,6 @@ dependencies:
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 - jupyter-resource-usage==0.7.0
 - jupyterlab==3.4.8
-- jupyterhub-singleuser==1.5.0
+- jupyterhub-singleuser==3.1.1
 - notebook==6.4.12
 - nteract_on_jupyter==2.1.3

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+# Frozen on 2023-02-03 12:31:38 UTC
+# Generated by conda-lock.
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repo2docker/buildpacks/conda/environment.py-3.11.yml

@@ -0,0 +1,15 @@
+# AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
+# Generated on 2023-02-03 12:31:38 UTC
+channels:
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+- pip
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+- notebook==6.4.12
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repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock

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repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock

@@ -1,41 +1,33 @@
 # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
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+# Frozen on 2023-02-03 12:33:35 UTC
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+https://conda.anaconda.org/conda-forge/noarch/bleach-6.0.0-pyhd8ed1ab_0.conda#d48b143d01385872a88ef8417e96c30e
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@@ -130,19 +121,19 @@ https://conda.anaconda.org/conda-forge/linux-aarch64/ipython-7.33.0-py37hd9ded2f
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repo2docker/buildpacks/conda/environment.py-3.7.yml

@@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-01-23 11:59:03 UTC
+# Generated on 2023-02-03 12:33:27 UTC
 channels:
 - conda-forge
 dependencies:
@@ -10,6 +10,6 @@ dependencies:
 - jupyter-offlinenotebook==0.2.2
 - jupyter-resource-usage==0.7.0
 - jupyterlab==3.4.8
-- jupyterhub-singleuser==1.5.0
+- jupyterhub-singleuser==3.1.1
 - notebook==6.4.12
 - nteract_on_jupyter==2.1.3

repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock

@@ -1,22 +1,19 @@
 # AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-01-23 12:02:13 UTC
+# Frozen on 2023-02-03 12:32:57 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 3ee9f169b42eac9c4b87b9717811f649e435daf083090ac5504090183c941cce
+# input_hash: 2fe7881a5392503fd6a9f83c6e0faba6d5cc08834c94af8545dde81cf2a35991
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@@ -24,20 +21,16 @@ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar
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@@ -45,18 +38,17 @@ https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_3.conda#5
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@@ -66,7 +58,7 @@ https://conda.anaconda.org/conda-forge/noarch/pandocfilters-1.5.0-pyhd8ed1ab_0.t
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 # AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY
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repo2docker/buildpacks/conda/environment.py-3.8.yml

@@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-01-23 12:02:13 UTC
+# Generated on 2023-02-03 12:32:57 UTC
 channels:
 - conda-forge
 dependencies:
@@ -10,6 +10,6 @@ dependencies:
 - jupyter-offlinenotebook==0.2.2
 - jupyter-resource-usage==0.7.0
 - jupyterlab==3.4.8
-- jupyterhub-singleuser==1.5.0
+- jupyterhub-singleuser==3.1.1
 - notebook==6.4.12
 - nteract_on_jupyter==2.1.3

repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock

@@ -1,12 +1,12 @@
 # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-01-23 12:05:17 UTC
+# Frozen on 2023-02-03 12:34:00 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 3e8d6c21102d42dc26862fa21fbba8f868f97a08b274d8fb41d88a36b73e8c77
+# input_hash: 579c1dd71f26268bb3c6470a6fbedf23ee639f53ae70be703248160e72e6ccdf
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@@ -46,18 +39,17 @@ https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_3.conda#5
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@@ -67,7 +59,7 @@ https://conda.anaconda.org/conda-forge/noarch/pandocfilters-1.5.0-pyhd8ed1ab_0.t
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repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock

@@ -1,11 +1,11 @@
 # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY
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@@ -66,7 +58,7 @@ https://conda.anaconda.org/conda-forge/noarch/pandocfilters-1.5.0-pyhd8ed1ab_0.t
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-https://conda.anaconda.org/conda-forge/noarch/prometheus_client-0.15.0-pyhd8ed1ab_0.tar.bz2#b260ed41427dbbe70537b3030c643b2e
+https://conda.anaconda.org/conda-forge/noarch/prometheus_client-0.16.0-pyhd8ed1ab_0.conda#8efaddc1c8b8ce262c4d1a7c6571c799
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@@ -80,25 +72,25 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f
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-https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567
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@@ -107,51 +99,51 @@ https://conda.anaconda.org/conda-forge/noarch/jedi-0.18.2-pyhd8ed1ab_0.conda#b5e
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-https://conda.anaconda.org/conda-forge/noarch/pip-22.3.1-pyhd8ed1ab_0.tar.bz2#da66f2851b9836d3a7c5190082a45f7d
-https://conda.anaconda.org/conda-forge/linux-aarch64/pycurl-7.45.1-py39h8b5e024_3.tar.bz2#08d1b183f4500bc6c997834f0792f2d5
+https://conda.anaconda.org/conda-forge/noarch/pip-23.0-pyhd8ed1ab_0.conda#85b35999162ec95f9f999bac15279c02
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repo2docker/buildpacks/conda/environment.py-3.9.yml

@@ -1,5 +1,5 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-01-23 12:05:17 UTC
+# Generated on 2023-02-03 12:34:00 UTC
 channels:
 - conda-forge
 dependencies:
@@ -10,6 +10,6 @@ dependencies:
 - jupyter-offlinenotebook==0.2.2
 - jupyter-resource-usage==0.7.0
 - jupyterlab==3.4.8
-- jupyterhub-singleuser==1.5.0
+- jupyterhub-singleuser==3.1.1
 - notebook==6.4.12
 - nteract_on_jupyter==2.1.3

repo2docker/buildpacks/conda/environment.yml

@@ -8,6 +8,6 @@ dependencies:
   - jupyter-offlinenotebook==0.2.2
   - jupyter-resource-usage==0.7.0
   - jupyterlab==3.4.8
-  - jupyterhub-singleuser==1.5.0
+  - jupyterhub-singleuser==3.1.1
   - notebook==6.4.12
   - nteract_on_jupyter==2.1.3

repo2docker/buildpacks/conda/freeze.py

@@ -117,7 +117,7 @@ if __name__ == "__main__":
         "py",
         nargs="*",
         help="Python version(s) to update and freeze",
-        default=("3.7", "3.8", "3.9", "3.10"),
+        default=("3.7", "3.8", "3.9", "3.10", "3.11"),
     )
     parser.add_argument(
         "platform",

repo2docker/buildpacks/conda/requirements.py-3.5.pip

@@ -1,17 +0,0 @@
-# pip-installed packages for Python 3.5
-# these should only be packages
-# whose versions are too new to have builds available for Python 3.5
-alembic==1.0.3
-async-generator==1.10
-chardet==3.0.4
-idna==2.7
-jupyterhub==0.9.4
-mako==1.0.7
-notebook==5.7.8
-nteract-on-jupyter==1.9.6
-pamela==0.3.0
-python-editor==1.0.3
-python-oauth2==1.1.0
-requests==2.20.1
-sqlalchemy==1.2.14
-urllib3==1.24.1

repo2docker/buildpacks/julia/julia_require.py

@@ -82,6 +82,14 @@ class JuliaRequireBuildPack(PythonBuildPack):
         else:
             julia_arch = "x86_64"
             julia_arch_short = "x64"
+
+        if V(self.julia_version) < V("0.7"):
+            # IJulia with Julia 0.6 isn't compatible with more recent jupyter-core
+            # point it to the one in the kernel env
+            # I _think_ this is only relevant during installation
+            jupyter = "${KERNEL_PYTHON_PREFIX}/bin/jupyter"
+        else:
+            jupyter = "${NB_PYTHON_PREFIX}/bin/jupyter"
         return super().get_build_env() + [
             ("JULIA_PATH", "${APP_BASE}/julia"),
             ("JULIA_HOME", "${JULIA_PATH}/bin"),  # julia <= 0.6
@@ -91,7 +99,7 @@ class JuliaRequireBuildPack(PythonBuildPack):
             ("JULIA_VERSION", self.julia_version),
             ("JULIA_ARCH", julia_arch),
             ("JULIA_ARCH_SHORT", julia_arch_short),
-            ("JUPYTER", "${NB_PYTHON_PREFIX}/bin/jupyter"),
+            ("JUPYTER", jupyter),
         ]
 
     def get_path(self):

repo2docker/buildpacks/pipfile/__init__.py

@@ -113,8 +113,8 @@ class PipfileBuildPack(CondaBuildPack):
         # environment.
         assemble_scripts = super().get_assemble_scripts()
 
-        if self.py2:
-            # using Python 2 as a kernel, but Python 3 for the notebook server
+        if self.separate_kernel_env:
+            # using legacy Python (e.g. 2.7) as a kernel
 
             # requirements3.txt allows for packages to be installed to the
             # notebook servers Python environment

repo2docker/buildpacks/python/__init__.py

@@ -45,8 +45,8 @@ class PythonBuildPack(CondaBuildPack):
         # whether it's distinct from the notebook or the same.
         pip = "${KERNEL_PYTHON_PREFIX}/bin/pip"
         scripts = []
-        if self.py2:
-            # using python 2 kernel,
+        if self.separate_kernel_env:
+            # using legacy Python kernel
             # requirements3.txt allows installation in the notebook server env
             nb_requirements_file = self.binder_path("requirements3.txt")
             if os.path.exists(nb_requirements_file):

tests/conda/py35-binder-dir/verify

@@ -1,17 +1,28 @@
 #!/usr/bin/env python
+import os
 import sys
-from subprocess import check_output
+from subprocess import STDOUT, check_output
 
-assert sys.version_info[:2] == (3, 5), sys.version
+assert sys.version_info[:2] == (3, 7), sys.version
 
-out = check_output(["micromamba", "--version"]).decode("utf8").strip()
+
+def sh(cmd, **kwargs):
+    return check_output(cmd, **kwargs).decode("utf8").strip()
+
+
+kernel_python = os.path.join(os.environ["KERNEL_PYTHON_PREFIX"], "bin", "python")
+out = sh([kernel_python, "--version"], stderr=STDOUT)
+v = out.split()[1]
+assert v[:3] == "3.5", out
+
+out = sh(["micromamba", "--version"])
 assert out == "1.1.0", out
 
-out = check_output(["mamba", "--version"]).decode("utf8").strip()
+out = sh(["mamba", "--version"])
 assert (
     out
     == """mamba 1.1.0
 conda 4.13.0"""
 ), out
 
-import numpy
+sh([kernel_python, "-c", "import numpy"])

tests/conda/py36-postBuild/environment.yml

@@ -0,0 +1,3 @@
+dependencies:
+  - python=3.6
+  - numpy

tests/conda/py36-postBuild/postBuild

@@ -0,0 +1,9 @@
+#!/bin/bash
+set -ex
+
+# mamba/conda installs in kernel env
+mamba install -y make
+
+# note `pip` on path is _not_ the kernel env!
+# is this what we (or users) want?
+pip install pytest

tests/conda/py36-postBuild/verify

@@ -0,0 +1,3 @@
+#!/bin/bash
+set -ex
+pytest -vs ./verify.py

tests/conda/py36-postBuild/verify.py

@@ -0,0 +1,85 @@
+"""
+tests to be run with pytest inside the container
+
+can't be called test_whatever.py because then _host_ pytest will try to run it!
+"""
+
+import json
+import os
+import shutil
+from subprocess import check_output
+
+from pytest import fixture
+
+kernel_prefix = os.environ.get("KERNEL_PYTHON_PREFIX")
+server_prefix = os.environ.get("NB_PYTHON_PREFIX")
+
+
+def json_cmd(cmd):
+    """Run a command and decode its JSON output"""
+    out = check_output(cmd)
+    return json.loads(out.decode("utf8", "replace"))
+
+
+def conda_pkgs(prefix):
+    """Conda package list as a dict"""
+    conda_json = json_cmd(["conda", "list", "--json", "-p", prefix])
+    return {pkg["name"]: pkg for pkg in conda_json}
+
+
+def pip_pkgs(prefix):
+    """Pip package list as a dict"""
+    pip_json = json_cmd([f"{prefix}/bin/pip", "list", "--format=json"])
+    return {pkg["name"]: pkg for pkg in pip_json}
+
+
+@fixture(scope="session")
+def kernel_conda():
+    return conda_pkgs(kernel_prefix)
+
+
+@fixture(scope="session")
+def server_conda():
+    return conda_pkgs(server_prefix)
+
+
+@fixture(scope="session")
+def kernel_pip():
+    return pip_pkgs(kernel_prefix)
+
+
+@fixture(scope="session")
+def server_pip():
+    return pip_pkgs(server_prefix)
+
+
+def test_which_python():
+    # server python comes first. Is this expected?
+    assert shutil.which("python3") == f"{server_prefix}/bin/python3"
+
+
+def test_kernel_env(kernel_conda):
+    assert kernel_prefix != server_prefix
+    kernel_python = kernel_conda["python"]["version"]
+    assert kernel_python[:3] == "3.6"
+    # test environment.yml packages
+    assert "numpy" in kernel_conda
+
+
+def test_server_env(server_conda):
+    # this should be the default version
+    # it will need updating when the default changes
+    assert server_conda["python"]["version"][:3] == "3.7"
+
+
+def test_conda_install(kernel_conda, server_conda):
+    # test that postBuild conda install went in the kernel env
+    assert "make" in kernel_conda
+    assert "make" not in server_conda
+
+
+def test_pip_install(kernel_pip, server_pip):
+    # server env comes first for pip
+    # is this expected?
+    assert "pytest" not in kernel_pip
+    assert "pytest" in server_pip

tests/external/reproductions.repos.yaml

@@ -33,7 +33,7 @@
 # Zenodo record of https://github.com/binder-examples/requirements
 - name: 10.5281/zenodo.3242074
   url: 10.5281/zenodo.3242074
-  verify: python -c 'import matplotlib'
+  verify: /srv/conda/envs/kernel/bin/python -c 'import matplotlib'
 # Test that files in git-lfs are properly cloned
 - name: LFS
   url: https://github.com/binderhub-ci-repos/lfs

tests/pipfile/py36/verify

@@ -1,8 +1,8 @@
-#!/usr/bin/env python
+#!/srv/conda/envs/kernel/bin/python
 import sys
 
-import pypi_pkg_test
-import there
-
 print(sys.version_info)
 assert sys.version_info[:2] == (3, 6)
+
+import pypi_pkg_test  # noqa
+import there  # noqa

tests/venv/py35/verify

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/srv/conda/envs/kernel/bin/python
 import sys
 
 print(sys.version_info)