Merge remote-tracking branch 'origin/main' into new-default

Author: minrk

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 @@ def get_path(self):
         """
         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 @@ def get_build_script_files(self):
         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 @@ def uses_r(self):
     @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 @@ def get_env_scripts(self):
         """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 @@ def get_env_scripts(self):
                     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
                     """,
                 ),

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

@@ -1,8 +1,8 @@
-# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY
-# Frozen on 2023-02-03 15:07:27 UTC
+# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY
+# Frozen on 2023-02-03 12:33:27 UTC
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 319256a4b378b6d51346c17bd2d31c0d9cd69bc3c1d10cd858de62da107fc85a
+# input_hash: 56d66ed1f6b5535bd09b3fb8546cc5bdb3cea65aa2ed89ffaf52424a63c739aa
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080
@@ -13,11 +13,7 @@ https://conda.anaconda.org/conda-forge/noarch/tzdata-2022g-h191b570_0.conda#51fc
 https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
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-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2#f26ef8098fab1f719c91eb760d63381a
 https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed
-https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
-https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3
 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206
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@@ -27,18 +23,15 @@ https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz
 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4acfc691e64342b9dae57cf2adc63238
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-https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.51.0-hff17c54_0.conda#dd682f0b6d65e75b2bc868fc8e93d87e
 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2#2e5f9a37d487e1019fd4d8113adb2f9f
-https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-hf14f497_3.tar.bz2#d85acad4b47dff4e3def14a769a97906
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 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2#4b11e365c0275b808be78b30f904e295
-https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-h81ceb04_0.conda#89a41adce7106749573d883b2f657d78
 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
+https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.40.0-h4ff8645_0.tar.bz2#bb11803129cbbb53ed56f9506ff74145
+https://conda.anaconda.org/conda-forge/linux-64/python-3.7.12-hf930737_100_cpython.tar.bz2#416558a6f46b7a1fa8db7d0e98aff56a
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@@ -68,7 +61,7 @@ https://conda.anaconda.org/conda-forge/noarch/parso-0.8.3-pyhd8ed1ab_0.tar.bz2#1
 https://conda.anaconda.org/conda-forge/noarch/pickleshare-0.7.5-py_1003.tar.bz2#415f0ebb6198cc2801c73438a9fb5761
 https://conda.anaconda.org/conda-forge/noarch/pkgutil-resolve-name-1.3.10-pyhd8ed1ab_0.tar.bz2#89e3c7cdde7d3aaa2aee933b604dd07f
 https://conda.anaconda.org/conda-forge/noarch/prometheus_client-0.16.0-pyhd8ed1ab_0.conda#8efaddc1c8b8ce262c4d1a7c6571c799
-https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.4-py310h5764c6d_0.tar.bz2#c3c55664e9becc48e6a652e2b641961f
+https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.3-py37h540881e_0.tar.bz2#0c813ad118e926df328bf74899a48047
 https://conda.anaconda.org/conda-forge/noarch/ptyprocess-0.7.0-pyhd3deb0d_0.tar.bz2#359eeb6536da0e687af562ed265ec263
 https://conda.anaconda.org/conda-forge/noarch/pure_eval-0.2.2-pyhd8ed1ab_0.tar.bz2#6784285c7e55cb7212efabc79e4c2883
 https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2#076becd9e05608f8dc72757d5f3a91ff
@@ -86,7 +79,7 @@ https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5
 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303
 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae
 https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2#5844808ffab9ebdb694585b50ba02a96
-https://conda.anaconda.org/conda-forge/linux-64/tornado-6.2-py310h5764c6d_1.tar.bz2#be4a201ac582c11d89ed7d15b3157cc3
+https://conda.anaconda.org/conda-forge/linux-64/tornado-6.2-py37h540881e_0.tar.bz2#2f0863ba6b29d1d2872b064dd697a492
 https://conda.anaconda.org/conda-forge/noarch/traitlets-5.9.0-pyhd8ed1ab_0.conda#d0b4f5c87cd35ac3fb3d47b223263a64
 https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.4.0-pyha770c72_0.tar.bz2#2d93b130d148d7fc77e583677792fc6a
 https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-py_1.tar.bz2#3563be4c5611a44210d9ba0c16113136
@@ -100,16 +93,14 @@ https://conda.anaconda.org/conda-forge/noarch/babel-2.11.0-pyhd8ed1ab_0.tar.bz2#
 https://conda.anaconda.org/conda-forge/noarch/backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0.tar.bz2#c5b3edc62d6309088f4970b3eaaa65a6
 https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.11.2-pyha770c72_0.conda#88b59f6989f0ed5ab3433af0b82555e1
 https://conda.anaconda.org/conda-forge/noarch/bleach-6.0.0-pyhd8ed1ab_0.conda#d48b143d01385872a88ef8417e96c30e
-https://conda.anaconda.org/conda-forge/linux-64/cffi-1.15.1-py310h255011f_3.conda#800596144bb613cd7ac58b80900ce835
-https://conda.anaconda.org/conda-forge/noarch/comm-0.1.2-pyhd8ed1ab_0.conda#3c78af4752bb1600ebe5e83ef4588eaa
-https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-6.0.0-pyha770c72_0.conda#691644becbcdca9f73243450b1c63e62
+https://conda.anaconda.org/conda-forge/linux-64/cffi-1.15.1-py37h43b0acd_1.tar.bz2#5111b64bdfdd72d85086ec49c952fe0d
+https://conda.anaconda.org/conda-forge/linux-64/importlib-metadata-4.11.4-py37h89c1867_0.tar.bz2#71107630527e4bd82932952351231efe
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 https://conda.anaconda.org/conda-forge/noarch/jedi-0.18.2-pyhd8ed1ab_0.conda#b5e695ef9c3f0d27d6cd96bf5adc9e07
 https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.2-pyhd8ed1ab_1.tar.bz2#c8490ed5c70966d232fdd389d0dbed37
 https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.1.6-pyhd8ed1ab_0.tar.bz2#b21613793fcc81d944c76c9f2864a7de
 https://conda.anaconda.org/conda-forge/noarch/pexpect-4.8.0-pyh1a96a4e_2.tar.bz2#330448ce4403cc74990ac07c555942a1
 https://conda.anaconda.org/conda-forge/noarch/pip-23.0-pyhd8ed1ab_0.conda#85b35999162ec95f9f999bac15279c02
-https://conda.anaconda.org/conda-forge/linux-64/pycurl-7.45.1-py310h60f9ec7_3.tar.bz2#ffa28fea807396092a45cd450efdcc97
 https://conda.anaconda.org/conda-forge/noarch/pygments-2.14.0-pyhd8ed1ab_0.conda#c78cd16b11cd6a295484bd6c8f24bea1
 https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2#dd999d1cc9f79e67dbb855c8924c7984
 https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml-0.17.21-py310h5764c6d_2.tar.bz2#93643151fba5c31c676effdd7661f075
@@ -139,13 +130,12 @@ https://conda.anaconda.org/conda-forge/noarch/ipython-8.9.0-pyh41d4057_0.conda#3
 https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.0.2-pyhd8ed1ab_0.conda#cbb8d182b6053ce14b5fe60ef1e36fbb
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 https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.14-pyhd8ed1ab_0.conda#01f33ad2e0aaf6b5ba4add50dad5ad29
-https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.21.1-pyh210e3f2_0.conda#225e7869419b8bcae5d3165eba50204d
-https://conda.anaconda.org/conda-forge/noarch/nbclient-0.7.2-pyhd8ed1ab_0.conda#6c7b0d75b66a220274bb5a28c23197f2
+https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.16.2-pyh210e3f2_0.tar.bz2#6b0f40821b784cac8a33d0c5eb7602c0
+https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.9-pyhd8ed1ab_0.conda#a9e1826152e79416db71c51b0d3af28c
 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/linux-64/jupyterhub-base-1.5.0-py310hff52083_1.tar.bz2#3d2e9d7f52b0274fd4f9d608cfb750a5
-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/jupyter_server-1.23.4-pyhd8ed1ab_0.conda#35b7e9267926e864cc70ce137e6588ca
+https://conda.anaconda.org/conda-forge/noarch/jupyterhub-base-3.1.1-pyh2a2186d_0.conda#78fc5dfd4577a7ba172fa65eb64b6afb
 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
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@@ -154,6 +144,6 @@ https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.2-pyhd8ed1ab_0.t
 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-64/jupyterhub-singleuser-1.5.0-py310hff52083_1.tar.bz2#1d878f40d50406b5aa51348b3e65525b
 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