Merge remote-tracking branch 'upstream/main' into feat/new-base

2023-03-23 22:21:02 +05:30 · 2023-03-23 22:21:02 +05:30 · 5894f63b87
commit 5894f63b87
--- a/.codecov.yml
+++ b/.codecov.yml
@ -6,7 +6,7 @@ coverage:
  status:
    project:
      default:
-        target: auto
+        target: "0%"
    patch:
      default:
-        target: 20%
+        target: "0%"
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@ -11,6 +11,7 @@ on:
      - "**.rst"
      - ".github/workflows/*"
      - "!.github/workflows/docker.yml"
+      - ".pre-commit-config.yaml"
  push:
    paths-ignore:
      - "docs/**"
@ -18,6 +19,7 @@ on:
      - "**.rst"
      - ".github/workflows/*"
      - "!.github/workflows/docker.yml"
+      - ".pre-commit-config.yaml"
    branches-ignore:
      - "dependabot/**"
      - "pre-commit-ci-update-config"
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@ -11,6 +11,7 @@ on:
      - "**.rst"
      - ".github/workflows/*"
      - "!.github/workflows/release.yml"
+      - ".pre-commit-config.yaml"
  push:
    paths-ignore:
      - "docs/**"
@ -18,6 +19,7 @@ on:
      - "**.rst"
      - ".github/workflows/*"
      - "!.github/workflows/release.yml"
+      - ".pre-commit-config.yaml"
    branches-ignore:
      - "dependabot/**"
      - "pre-commit-ci-update-config"
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@ -11,6 +11,7 @@ on:
      - "**.rst"
      - ".github/workflows/*"
      - "!.github/workflows/test.yml"
+      - ".pre-commit-config.yaml"
  push:
    paths-ignore:
      - "docs/**"
@ -18,6 +19,7 @@ on:
      - "**.rst"
      - ".github/workflows/*"
      - "!.github/workflows/test.yml"
+      - ".pre-commit-config.yaml"
    branches-ignore:
      - "dependabot/**"
      - "pre-commit-ci-update-config"
--- a/.gitpod.yml
+++ b/.gitpod.yml
@ -1,10 +1,12 @@
 tasks:
  - init: |
      pip3 install sphinx-autobuild
+      pip3 install -r dev-requirements.txt
      pip3 install -r docs/requirements.txt
      pip3 install -e .
    command: |
      sphinx-autobuild docs/source/ docs/_build/html/
    name: Sphinx preview
+      
 ports:
  - port: 8000
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@ -23,7 +23,7 @@ repos:

  # Autoformat: Python code
  - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
    hooks:
      - id: black
        args:
@ -36,7 +36,7 @@ repos:

  # Autoformat: Python code
  - repo: https://github.com/pycqa/isort
-    rev: 5.11.4
+    rev: 5.12.0
    hooks:
      - id: isort
        args:
@ -44,7 +44,7 @@ repos:

  # Autoformat: markdown
  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.4
+    rev: v3.0.0-alpha.6
    hooks:
      - id: prettier
        files: ".md"
--- a/docs/source/config_files.rst
+++ b/docs/source/config_files.rst
@ -43,8 +43,8 @@ specified in your ``environment.yml``.
 You can also specify which Python version to install in your built environment
 with ``environment.yml``. By default, ``repo2docker`` installs
 |default_python| with your ``environment.yml`` unless you include the version of
-Python in this file.  ``conda`` supports all versions of Python,
-though ``repo2docker`` support is best with Python 3.7, 3.6, 3.5 and 2.7.
+Python in this file.  ``conda`` Should support all versions of Python,
+though ``repo2docker`` support is best with Python 3.7-3.11.

 .. warning::
   If you include a Python version in a ``runtime.txt`` file in addition to your
--- a/docs/source/faq.rst
+++ b/docs/source/faq.rst
@ -22,6 +22,10 @@ Repo2docker officially supports the following versions of Python
 (specified in your :ref:`environment.yml <environment.yml>` or
 :ref:`runtime.txt <runtime.txt>` file):

+- 3.11 (added in 2023)
+- 3.10 (added in 2022, default in 2023)
+- 3.9 (added in 2021)
+- 3.8 (added in 0.11)
 - 3.7 (added in 0.7, default in 0.8)
 - 3.6 (default in 0.7 and earlier)
 - 3.5
@ -35,9 +39,18 @@ in the base environment is not packaged for your Python,
 either because the version of the package is too new and your chosen Python is too old,
 or vice versa.

-I Python 2.7 is specified, a separate environment for the kernel will be
-installed with Python 2. The notebook server will run in the default Python 3.7
-environment.
+If an old version of Python is specified (3.6 or earlier in 2023), a separate environment for the kernel will be installed with your requested Python version.
+The notebook server will run in the default |default_python| environment.
+That is, your _notebooks_ will run with Python 3.6, while your notebook _server_ will run with |default_python|.
+
+These two environments can be distinguished with ``$NB_PYTHON_PREFIX/bin/python`` for the server and ``$KERNEL_PYTHON_PREFIX/bin/python`` for the kernel.
+Both of these environment variables area always defined, even when they are the same.
+
+Starting in 2023, the default version of Python used when Python version is unspecified will be updated more often.
+Python itself releases a new version every year now, and repo2docker will follow, with the default Python version generally trailing the latest stable version of Python itself by 1-2 versions.
+
+If you choose not to specify a Python version, your repository is _guaranteed_ to stop working, eventually.
+We **strongly** recommend specifying a Python version (in environment.yml, runtime.txt, Pipfile, etc.)

 Julia
 ~~~~~
--- a/repo2docker/buildpacks/conda/init.py
+++ b/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
@ -141,7 +143,7 @@ class CondaBuildPack(BaseImage):
            ),
        ]

-    major_pythons = {"2": "2.7", "3": "3.7"}
+    major_pythons = {"2": "2.7", "3": "3.10"}

    def get_build_script_files(self):
        """
@ -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
@ -396,6 +424,7 @@ class CondaBuildPack(BaseImage):
                    echo auth-none=1 >> /etc/rstudio/rserver.conf && \
                    echo auth-minimum-user-id=0 >> /etc/rstudio/rserver.conf && \
                    echo "rsession-which-r={env_prefix}/bin/R" >> /etc/rstudio/rserver.conf && \
+                    echo "rsession-ld-library-path={env_prefix}/lib" >> /etc/rstudio/rserver.conf && \
                    echo www-frame-origin=same >> /etc/rstudio/rserver.conf
                    """,
                ),
--- a/repo2docker/buildpacks/conda/environment-linux-64.lock
+++ b/repo2docker/buildpacks/conda/environment-linux-64.lock
@ -1,43 +1,37 @@
-# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-01-01 11:29:43 UTC
+# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY
+# Frozen on 2023-02-03 12:34:24 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: f39cf3a86cdaeb58bee45974ccbdaf3fb51ad41f0bb6f3caf9340c5aad0dfa3b
+# input_hash: 9fd16b0f6d64e86a62e326694b74a429aef5dd7b227a96b4f0e2425851e4e016
@EXPLICIT
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-https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.7-3_cp37m.conda#46277e9cf1ecd46926a31cea47079009
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+https://conda.anaconda.org/conda-forge/linux-64/nodejs-18.12.1-h8839609_0.tar.bz2#305f25b78340b0f7b391a6919d1246f2
+https://conda.anaconda.org/conda-forge/linux-64/python-3.10.9-he550d4f_0_cpython.conda#3cb3e91b3fe66baa68a12c85f39b9b40
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--- a/repo2docker/buildpacks/conda/environment-linux-aarch64.lock
+++ b/repo2docker/buildpacks/conda/environment-linux-aarch64.lock
@ -1,42 +1,36 @@
-# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-01-01 11:29:53 UTC
+# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY
+# Frozen on 2023-02-03 12:34:31 UTC
 # Generated by conda-lock.
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-# input_hash: a623ebdc4f4a6b9c05e667ad83a83f99bc96451d4d23e680cd12966e0398a255
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--- a/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock
@ -1,12 +1,12 @@
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--- a/repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock
+++ b/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
-# Frozen on 2023-01-01 11:31:25 UTC
+# Frozen on 2023-02-03 12:34:31 UTC
 # Generated by conda-lock.
 # platform: linux-aarch64
-# input_hash: 59cb7ad4d24f6fd004450247a9c3ff6b1ea1de27c1549ce5efea1a397c6b6f20
+# input_hash: c039d9a57d204f210d3832a8744df6e5ed536030655439a29ff883148f704b60
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--- a/repo2docker/buildpacks/conda/environment.py-3.10.yml
+++ b/repo2docker/buildpacks/conda/environment.py-3.10.yml
@ -1,15 +1,15 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-01-01 11:31:15 UTC
+# Generated on 2023-02-03 12:34:24 UTC
 channels:
 - conda-forge
 dependencies:
 - python=3.10.*
- nodejs=16
+- nodejs=18
 - pip
 - ipywidgets==8.0.2
 - jupyter-offlinenotebook==0.2.2
- jupyter-resource-usage==0.6.3
+- 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
--- a/repo2docker/buildpacks/conda/environment.py-3.11-linux-64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.11-linux-64.lock
@ -0,0 +1,150 @@
+# AUTO GENERATED FROM environment.py-3.11.yml, DO NOT MANUALLY MODIFY
+# Frozen on 2023-02-03 12:31:38 UTC
+# Generated by conda-lock.
+# platform: linux-64
+# input_hash: f7978ab1627d5ab9863bff89dd5c41d37073b0bac80171a2c092390857888902
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--- a/repo2docker/buildpacks/conda/environment.py-3.11.yml
+++ b/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:
+- conda-forge
+dependencies:
+- python=3.11.*
+- nodejs=18
+- pip
+- ipywidgets==8.0.2
+- jupyter-offlinenotebook==0.2.2
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+- notebook==6.4.12
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--- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock
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@ -1,42 +1,34 @@
 # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-01-01 11:29:43 UTC
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--- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock
+++ b/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
-# Frozen on 2023-01-01 11:29:53 UTC
+# Frozen on 2023-02-03 12:33:35 UTC
 # Generated by conda-lock.
 # platform: linux-aarch64
-# input_hash: a623ebdc4f4a6b9c05e667ad83a83f99bc96451d4d23e680cd12966e0398a255
+# input_hash: 5d827030b8550a7c54b1799a2f8975f8c422c8cd7f555193fcd4912380c6d3cb
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--- a/repo2docker/buildpacks/conda/environment.py-3.7.yml
+++ b/repo2docker/buildpacks/conda/environment.py-3.7.yml
@ -1,15 +1,15 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-01-01 11:29:43 UTC
+# Generated on 2023-02-03 12:33:27 UTC
 channels:
 - conda-forge
 dependencies:
 - python=3.7.*
- nodejs=16
+- nodejs=18
 - pip
 - ipywidgets==8.0.2
 - jupyter-offlinenotebook==0.2.2
- jupyter-resource-usage==0.6.3
+- 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
--- a/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock
+++ b/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 2023-01-01 11:30:13 UTC
+# Frozen on 2023-02-03 12:32:57 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: e67091c1a370df5b722565831d5e32ce5255b1c0c7faeeed6baa7d7ee7694693
+# input_hash: 2fe7881a5392503fd6a9f83c6e0faba6d5cc08834c94af8545dde81cf2a35991
@EXPLICIT
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--- a/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock
+++ b/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock
@ -1,11 +1,11 @@
 # AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-01-01 11:30:24 UTC
+# Frozen on 2023-02-03 12:33:06 UTC
 # Generated by conda-lock.
 # platform: linux-aarch64
-# input_hash: e139b00bb524dd3e51bfc01017ff16a33a572342066e437c1aef0a5a631c678d
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--- a/repo2docker/buildpacks/conda/environment.py-3.8.yml
+++ b/repo2docker/buildpacks/conda/environment.py-3.8.yml
@ -1,15 +1,15 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-01-01 11:30:13 UTC
+# Generated on 2023-02-03 12:32:57 UTC
 channels:
 - conda-forge
 dependencies:
 - python=3.8.*
- nodejs=16
+- nodejs=18
 - pip
 - ipywidgets==8.0.2
 - jupyter-offlinenotebook==0.2.2
- jupyter-resource-usage==0.6.3
+- 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
--- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock
+++ b/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 2023-01-01 11:30:44 UTC
+# Frozen on 2023-02-03 12:34:00 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: f0b7020f912d4c25c1482bcd0774212f9f4f041ec6eaea0b34676693729dcaf0
+# input_hash: 579c1dd71f26268bb3c6470a6fbedf23ee639f53ae70be703248160e72e6ccdf
@EXPLICIT
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@ -25,21 +22,16 @@ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar
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-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.7-h0b41bf4_1.conda#7adaac6ff98219bcb99b45e408b80f4e
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+https://conda.anaconda.org/conda-forge/linux-64/nodejs-18.12.1-h8839609_0.tar.bz2#305f25b78340b0f7b391a6919d1246f2
+https://conda.anaconda.org/conda-forge/linux-64/python-3.9.16-h2782a2a_0_cpython.conda#95c9b7c96a7fd7342e0c9d0a917b8f78
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@ -47,113 +39,112 @@ https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_3.conda#5
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--- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock
+++ b/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
-# Frozen on 2023-01-01 11:30:54 UTC
+# Frozen on 2023-02-03 12:34:07 UTC
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+# input_hash: 5d969695d1fb1e159afd55142ca58e173ba124b10a7223b9f8686786800aef5e
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+https://conda.anaconda.org/conda-forge/linux-aarch64/cryptography-39.0.0-py39h8a84b6a_0.conda#dbf0c4fe3e4cd291219b108e8d3deab6
+https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-6.0.0-hd8ed1ab_0.conda#a67d43e1527a37199dd8db913366f68e
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+https://conda.anaconda.org/conda-forge/linux-aarch64/sqlalchemy-2.0.1-py39h599bc27_0.conda#33bf0e134ca4279c03a71f8720931d82
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-https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.5-pyh9f0ad1d_2.tar.bz2#5266fcd697043c59621fda522b3d78ee
+https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.6-pyhd8ed1ab_0.conda#078979d33523cb477bd1916ce41aacc9
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-https://conda.anaconda.org/conda-forge/linux-aarch64/jupyter_core-5.1.1-py39h4420490_0.conda#000c9bd1bde07a73caf4e2b333faeb43
+https://conda.anaconda.org/conda-forge/linux-aarch64/jupyter_core-5.2.0-py39h4420490_0.conda#0febdd95c4b1080857f066ff497ba3c1
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-https://conda.anaconda.org/conda-forge/noarch/pyopenssl-22.1.0-pyhd8ed1ab_0.tar.bz2#fbfa0a180d48c800f922a10a114a8632
+https://conda.anaconda.org/conda-forge/noarch/pyopenssl-23.0.0-pyhd8ed1ab_0.conda#d41957700e83bbb925928764cb7f8878
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-https://conda.anaconda.org/conda-forge/noarch/ipython-8.7.0-pyh41d4057_0.conda#adc2f96edf35423c091dba93b642573a
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-https://conda.anaconda.org/conda-forge/noarch/nbformat-5.7.1-pyhd8ed1ab_0.conda#facb42913140f1a399a5ebb65b30915e
-https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.13-pyhd8ed1ab_0.conda#3078ef2359efd6ecadbc7e085c5e0592
-https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.19.4-pyh210e3f2_0.conda#65372b6dd819e2c36345cf91eeb4ff06
+https://conda.anaconda.org/conda-forge/noarch/ipython-8.9.0-pyh41d4057_0.conda#399217b9b00e59e990585576eeca3dde
+https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.0.2-pyhd8ed1ab_0.conda#cbb8d182b6053ce14b5fe60ef1e36fbb
+https://conda.anaconda.org/conda-forge/noarch/nbformat-5.7.3-pyhd8ed1ab_0.conda#9714111cb6c7dbbc9a9f34de205c2f29
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+https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.21.1-pyh210e3f2_0.conda#225e7869419b8bcae5d3165eba50204d
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-https://conda.anaconda.org/conda-forge/noarch/requests-2.28.1-pyhd8ed1ab_1.tar.bz2#089382ee0e2dc2eae33a04cc3c2bddb0
+https://conda.anaconda.org/conda-forge/noarch/requests-2.28.2-pyhd8ed1ab_0.conda#11d178fc55199482ee48d6812ea83983
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-https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.7-pyhd8ed1ab_0.conda#dce063b1f5d6193646fc2ac43f88b77f
-https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.4-pyhd8ed1ab_0.conda#35b7e9267926e864cc70ce137e6588ca
-https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.2.7-pyhd8ed1ab_0.conda#7d48776bb3fdfa6447267c413a480ccd
-https://conda.anaconda.org/conda-forge/noarch/jupyter-resource-usage-0.6.3-pyhd8ed1ab_0.tar.bz2#9d26ebd67e0e22aba13ac8a490d88d9e
-https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.17.0-pyhd8ed1ab_0.conda#68364b266a989bb9829943bfd33187d8
-https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.2.7-pyhd8ed1ab_0.conda#b019fe41e6f6b88e0557532514f39cff
+https://conda.anaconda.org/conda-forge/noarch/jupyterhub-base-3.1.1-pyh2a2186d_0.conda#78fc5dfd4577a7ba172fa65eb64b6afb
+https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.9-pyhd8ed1ab_0.conda#a9e1826152e79416db71c51b0d3af28c
+https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.5-pyhd8ed1ab_0.conda#e3ae1d46749f48a1875b560fca41cb0c
+https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.2.9-pyhd8ed1ab_0.conda#4a8dc94c7c2f3736dc4b91ec345d5b4b
+https://conda.anaconda.org/conda-forge/noarch/jupyter-resource-usage-0.7.0-pyhd8ed1ab_0.conda#c57567d49d926826b1f852712ac8acfa
+https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.19.0-pyhd8ed1ab_0.conda#9dc0706ec2f8e13b7a0db9d6a19051ff
+https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.2.9-pyhd8ed1ab_0.conda#523aaa3affb003ab0e68dbc24c9027f4
 https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.2-pyhd8ed1ab_0.tar.bz2#40be846cd4e78672a40e43db9dae753c
-https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.4.8-pyhd8ed1ab_0.tar.bz2#f4f150f83ed90a1b833e6081bbf38257
+https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.5.1-pyhd8ed1ab_0.conda#cf832e3d48ef22528c676ed6e4b4085a
 https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad
 https://conda.anaconda.org/conda-forge/noarch/jupyter-offlinenotebook-0.2.2-pyh1d7be83_0.tar.bz2#fe55056ce4bc4bd4953ba440270735fb
-https://conda.anaconda.org/conda-forge/linux-aarch64/jupyterhub-singleuser-1.5.0-py39ha65689a_1.tar.bz2#428f24f44794a428a875ee08be6eee31
 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-3.4.8-pyhd8ed1ab_0.tar.bz2#6fbf13b0e8a6fa24bbae91205e8ce467
 https://conda.anaconda.org/conda-forge/noarch/nteract_on_jupyter-2.1.3-py_0.tar.bz2#1430ccd983ae6b161e2fbf4377965f7a
+https://conda.anaconda.org/conda-forge/noarch/jupyterhub-singleuser-3.1.1-pyh2a2186d_0.conda#6d0a3394efe9ff7c0ad1ed03a6ca3720
--- a/repo2docker/buildpacks/conda/environment.py-3.9.yml
+++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml
@ -1,15 +1,15 @@
 # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY
-# Generated on 2023-01-01 11:30:44 UTC
+# Generated on 2023-02-03 12:34:00 UTC
 channels:
 - conda-forge
 dependencies:
 - python=3.9.*
- nodejs=16
+- nodejs=18
 - pip
 - ipywidgets==8.0.2
 - jupyter-offlinenotebook==0.2.2
- jupyter-resource-usage==0.6.3
+- 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
--- a/repo2docker/buildpacks/conda/environment.yml
+++ b/repo2docker/buildpacks/conda/environment.yml
@ -1,13 +1,13 @@
 channels:
  - conda-forge
 dependencies:
-  - python=3.7
-  - nodejs=16
+  - python=3.10
+  - nodejs=18
  - pip
  - ipywidgets==8.0.2
  - jupyter-offlinenotebook==0.2.2
-  - jupyter-resource-usage==0.6.3
+  - 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
--- a/repo2docker/buildpacks/conda/freeze.py
+++ b/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",
@ -126,7 +126,7 @@ if __name__ == "__main__":
        default=("linux-64", "linux-aarch64"),
    )
    args = parser.parse_args()
-    default_py = "3.7"
+    default_py = "3.10"
    for py in args.py:
        for platform in args.platform:
            env_file = pathlib.Path(str(ENV_FILE_T).format(py=py))
--- a/repo2docker/buildpacks/conda/install-base-env.bash
+++ b/repo2docker/buildpacks/conda/install-base-env.bash
@ -5,7 +5,7 @@ set -ex

 cd $(dirname $0)

-export MAMBA_VERSION=1.0.0
+export MAMBA_VERSION=1.1.0
 export CONDA_VERSION=4.13.0

 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2"
@ -34,6 +34,7 @@ channels:
 auto_update_conda: false
 show_channel_urls: true
 update_dependencies: false
+experimental_sat_error_message: true
 # channel_priority: flexible
 EOT

--- a/repo2docker/buildpacks/conda/requirements.py-3.5.pip
+++ b/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
--- a/repo2docker/buildpacks/julia/julia_require.py
+++ b/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):
--- a/repo2docker/buildpacks/nix/install-nix.bash
+++ b/repo2docker/buildpacks/nix/install-nix.bash
@ -2,11 +2,11 @@
 # This downloads and installs a pinned version of nix
 set -ex

-NIX_VERSION="2.3.9"
+NIX_VERSION="2.13.2"
 if [ "$NIX_ARCH" = "aarch64" ]; then
-  NIX_SHA256="733a26911193fdd44d5d68342075af5924d8c0701aae877e51a38d74ee9f4ff8"
+  NIX_SHA256="4ae275a46a2441d3459ae389a90ce6e8f7eff12c2a084b2d003ba6f8d0899603"
 else
-  NIX_SHA256="49763fd7fa06bcb712ced2f3f11afd275e3a4d7bc5ff0d6fd1d50a4c3ce7bbf4"
+  NIX_SHA256="beaec0f28899c22f33adbe30e4ecfceef87b797278c5210ee693e22e9719dfb4"
 fi

 # Do all our operations in /tmp, since we can't rely on current directory being writeable yet.
--- a/repo2docker/buildpacks/pipfile/init.py
+++ b/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
--- a/repo2docker/buildpacks/python/init.py
+++ b/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):
--- a/tests/base/node/verify
+++ b/tests/base/node/verify
@ -5,7 +5,7 @@ set -ex
 # check node system package and its version
 which node
 node --version
-node --version | grep v16
+node --version | grep v18

 which npm
 npm --version
--- a/tests/conda/downgrade/environment.yml
+++ b/tests/conda/downgrade/environment.yml
@ -0,0 +1,11 @@
+# originally xeus-cling@0.6.0
+# added python=3.9 pin because implicit downgrade of Python from 3.10 to 3.9 isn't allowed
+name: xeus-cling
+channels:
+  - conda-forge
+dependencies:
+  - python=3.9
+  - xeus-cling=0.6.0
+  - xtensor=0.20.8
+  - xtensor-blas=0.16.1
+  - notebook
--- a/tests/conda/downgrade/verify
+++ b/tests/conda/downgrade/verify
@ -0,0 +1,30 @@
+#!/usr/bin/env python3
+import json
+import pprint
+from subprocess import check_output
+
+
+def json_sh(cmd):
+    """Run a command that produces JSON on stdout and return the parsed result"""
+    buf = check_output(cmd)
+    return json.loads(buf.decode("utf8", "replace"))
+
+
+conda_pkg_list = json_sh(["conda", "list", "--json"])
+pprint.pprint(conda_pkg_list)
+# make it a dict
+pkgs = {pkg["name"]: pkg for pkg in conda_pkg_list}
+
+# base env resolved
+assert pkgs["python"]["version"].startswith("3.9"), pkgs["python"]
+assert "xeus-cling" in pkgs
+assert pkgs["xeus-cling"]["version"] == "0.6.0"
+
+# verify downgrade
+# this may be brittle, but it's unlikely any of these old versions
+# of packages will be rebuilt
+# xeus-cling 0.6.0 pins xeus 0.20, which pins openssl 1.1.1,
+# which in turn downgrades Python from >=3.9.16 to 3.9.6
+
+assert pkgs["openssl"]["version"].startswith("1.1.1"), pkgs["openssl"]["version"]
+assert pkgs["python"]["version"] == "3.9.6", pkgs["python"]["version"]
--- a/tests/conda/py-r-postbuild-file/verify.py
+++ b/tests/conda/py-r-postbuild-file/verify.py
@ -4,8 +4,8 @@ import sys


 def test_sys_version():
-    """The default python version should be 3.7"""
-    assert sys.version_info[:2] == (3, 7)
+    """The default python version should be 3.10"""
+    assert sys.version_info[:2] == (3, 10)


 def test_there():
--- a/tests/conda/py2/verify
+++ b/tests/conda/py2/verify
@ -1,7 +1,7 @@
 #!/usr/bin/env python
 import sys

-assert sys.version_info[:2] == (3, 7), sys.version
+assert sys.version_info[:2] == (3, 10), sys.version

 # verify that we have Python 2 and Python 3 kernelspecs
 from jupyter_client.kernelspec import KernelSpecManager
--- a/tests/conda/py35-binder-dir/verify
+++ b/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, 10), sys.version

-out = check_output(["micromamba", "--version"]).decode("utf8").strip()
-assert out == "1.0.0", out

-out = check_output(["mamba", "--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 = sh(["mamba", "--version"])
 assert (
    out
-    == """mamba 1.0.0
+    == """mamba 1.1.0
 conda 4.13.0"""
 ), out

-import numpy
+sh([kernel_python, "-c", "import numpy"])
--- a/tests/conda/py36-postBuild/environment.yml
+++ b/tests/conda/py36-postBuild/environment.yml
@ -0,0 +1,3 @@
+dependencies:
+  - python=3.6
+  - numpy
--- a/tests/conda/py36-postBuild/postBuild
+++ b/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
--- a/tests/conda/py36-postBuild/verify
+++ b/tests/conda/py36-postBuild/verify
@ -0,0 +1,3 @@
+#!/bin/bash
+set -ex
+pytest -vs ./verify.py
--- a/tests/conda/py36-postBuild/verify.py
+++ b/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"].split(".")[:2] == ["3", "10"]
+
+
+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
--- a/tests/external/reproductions.repos.yaml
+++ b/tests/external/reproductions.repos.yaml
@ -10,30 +10,24 @@
  ref: b8259dac9eb
  verify: python -c 'import matplotlib'
 # Test that a full remote/ref works
- name: Binder Examples - Requirements
+- name: Binder Examples - Requirements - origin/main
  url: https://github.com/binder-examples/requirements
  ref: origin/main
  verify: python -c 'import matplotlib'
 # Test that ref is added to branch if not present
- name: Binder Examples - Requirements
+- name: Binder Examples - Requirements - main
  url: https://github.com/binder-examples/requirements
  ref: main
  verify: python -c 'import matplotlib'
 # Test that tags work + ref is added to tag if not present
- name: Binder Examples - Requirements
+- name: Binder Examples - Requirements - tag
  url: https://github.com/binder-examples/requirements
-  ref: python-3.7
+  ref: python-3.8
  verify: python -c 'import matplotlib'
-# Test that custom channels and downgrades don't
-# get blocked by pinning
- name: Xeus-Cling
-  url: https://github.com/QuantStack/xeus-cling
-  ref: 0.6.0
-  verify: jupyter kernelspec list
 # 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
--- a/tests/pipfile/py36/verify
+++ b/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
--- a/tests/unit/contentproviders/test_dataverse.py
+++ b/tests/unit/contentproviders/test_dataverse.py
@ -95,7 +95,6 @@ def test_detect_dataverse(test_input, expected, requests_mock):

@pytest.fixture
 def dv_files(tmpdir):
-
    f1 = tmpdir.join("some-file.txt")
    f1.write("some content")

--- a/tests/unit/contentproviders/test_hydroshare.py
+++ b/tests/unit/contentproviders/test_hydroshare.py
@ -35,7 +35,6 @@ hydroshare_data = {


 def test_content_id(requests_mock):
-
    requests_mock.get(re.compile("https://"), json=hydroshare_data)
    requests_mock.get(re.compile("https://doi.org"), json=doi_resolver)

--- a/tests/venv/default/verify
+++ b/tests/venv/default/verify
@ -2,7 +2,7 @@
 # Verify that the default just provides a py3 environment with jupyter
 import sys

-assert sys.version_info[:2] == (3, 7), sys.version
+assert sys.version_info[:2] == (3, 10), sys.version
 import jupyter

 with open("/tmp/appendix") as f:
--- a/tests/venv/numpy/verify
+++ b/tests/venv/numpy/verify
@ -1,6 +1,6 @@
 #!/usr/bin/env python
 import sys

-assert sys.version_info[:2] == (3, 7)
+assert sys.version_info[:2] == (3, 10)

 import numpy
--- a/tests/venv/py35/verify
+++ b/tests/venv/py35/verify
@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/srv/conda/envs/kernel/bin/python
 import sys

 print(sys.version_info)