lockfiles need to be installed with conda create not conda env create

use different .lock filename extension, following conda-lock precedent

Could also follow .txt in conda docs!

conda env create -p prefix -f lock.txt *should* work,
but fails with errors about name being required,
but also fails if name is given due to conflict with `-p`

Author: minrk

repo2docker/buildpacks/conda/__init__.py

@@ -23,6 +23,14 @@ class CondaBuildPack(BaseImage):
 
     """
 
+    # The kernel environment file, if any.
+    # As an absolute path within the container.
+    _kernel_environment_file = ""
+
+    # The notebook server environment file, if any.
+    # As an absolute path within the container.
+    _nb_environment_file = ""
+
     def get_build_env(self):
         """Return environment variables to be set.
 
@@ -33,9 +41,15 @@ def get_build_env(self):
         env = super().get_build_env() + [
             ("CONDA_DIR", "${APP_BASE}/conda"),
             ("NB_PYTHON_PREFIX", "${CONDA_DIR}/envs/notebook"),
+            ("NB_ENVIRONMENT_FILE", self._nb_environment_file),
         ]
         if self.py2:
-            env.append(("KERNEL_PYTHON_PREFIX", "${CONDA_DIR}/envs/kernel"))
+            env.extend(
+                [
+                    ("KERNEL_PYTHON_PREFIX", "${CONDA_DIR}/envs/kernel"),
+                    ("KERNEL_ENVIRONMENT_FILE", self._kernel_environment_file),
+                ]
+            )
         else:
             env.append(("KERNEL_PYTHON_PREFIX", "${NB_PYTHON_PREFIX}"))
         return env
@@ -81,7 +95,7 @@ def get_build_scripts(self):
                 r"""
                 TIMEFORMAT='time: %3R' \
                 bash -c 'time /tmp/install-miniforge.bash' && \
-                rm /tmp/install-miniforge.bash /tmp/environment.yml
+                rm /tmp/install-miniforge.bash ${NB_ENVIRONMENT_FILE}
                 """,
             )
         ]
@@ -114,20 +128,25 @@ def get_build_script_files(self):
         # major Python versions during upgrade.
         # If no version is specified or no matching X.Y version is found,
         # the default base environment is used.
-        frozen_name = "environment.frozen.yml"
+        frozen_name = "environment.lock"
         if py_version:
             if self.py2:
                 # python 2 goes in a different env
                 files[
-                    "conda/environment.py-2.7.frozen.yml"
-                ] = "/tmp/kernel-environment.yml"
+                    "conda/environment.py-2.7.lock"
+                ] = self._kernel_environment_file = "/tmp/kernel-environment.lock"
             else:
-                py_frozen_name = "environment.py-{py}.frozen.yml".format(py=py_version)
-                if os.path.exists(os.path.join(HERE, py_frozen_name)):
-                    frozen_name = py_frozen_name
-                else:
-                    self.log.warning("No frozen env: %s", py_frozen_name)
-        files["conda/" + frozen_name] = "/tmp/environment.yml"
+                for ext in [".lock", ".frozen.yml"]:
+                    py_frozen_name = f"environment.py-{py_version}{ext}"
+                    if os.path.exists(os.path.join(HERE, py_frozen_name)):
+                        frozen_name = py_frozen_name
+                        break
+                if not frozen_name:
+                    self.log.warning(f"No frozen env for {py_version}")
+        _, frozen_ext = os.path.splitext(frozen_name)
+        files[
+            "conda/" + frozen_name
+        ] = self._nb_environment_file = f"/tmp/environment{frozen_ext}"
         files.update(super().get_build_script_files())
         return files
 

repo2docker/buildpacks/conda/environment.frozen.yml renamed to repo2docker/buildpacks/conda/environment.lock

@@ -22,18 +22,17 @@
 HERE = pathlib.Path(os.path.dirname(os.path.abspath(__file__)))
 
 ENV_FILE = HERE / "environment.yml"
-FROZEN_FILE = os.path.splitext(ENV_FILE)[0] + ".frozen.yml"
+FROZEN_FILE = os.path.splitext(ENV_FILE)[0] + ".lock"
 
 ENV_FILE_T = HERE / "environment.py-{py}.yml"
-FROZEN_FILE_T = os.path.splitext(ENV_FILE_T)[0] + ".frozen.yml"
 
 yaml = YAML(typ="rt")
 
 
 def freeze(env_file, frozen_file, platform="linux-64"):
-    """Freeze a conda environment.yml
+    """Freeze a conda environment
 
-    By running
+    By running:
 
         conda-lock --mamba --platform=linux-64 -f environment.yml
 
@@ -113,7 +112,7 @@ def set_python(py_env_file, py):
     for py in pys:
         env_file = pathlib.Path(str(ENV_FILE_T).format(py=py))
         set_python(env_file, py)
-        frozen_file = pathlib.Path(os.path.splitext(env_file)[0] + ".frozen.yml")
+        frozen_file = pathlib.Path(os.path.splitext(env_file)[0] + ".lock")
         freeze(env_file, frozen_file)
         if py == default_py:
             shutil.copy(frozen_file, FROZEN_FILE)

repo2docker/buildpacks/conda/environment.py-2.7.frozen.yml renamed to repo2docker/buildpacks/conda/environment.py-2.7.lock

@@ -45,21 +45,33 @@ conda config --system --set channel_priority "flexible"
 time mamba install -y mamba==${MAMBA_VERSION}
 
 echo "installing notebook env:"
-cat /tmp/environment.yml
-time mamba create --prefix ${NB_PYTHON_PREFIX} --file /tmp/environment.yml
+cat "${NB_ENVIRONMENT_FILE}"
+
+if [[ "${NB_ENVIRONMENT_FILE: -5}" == ".lock" ]]; then
+    create="mamba create"
+else
+    create="mamba env create"
+fi
+
+time $create -p ${NB_PYTHON_PREFIX} --file "${NB_ENVIRONMENT_FILE}"
 
 # empty conda history file,
 # which seems to result in some effective pinning of packages in the initial env,
 # which we don't intend.
 # this file must not be *removed*, however
 echo '' > ${NB_PYTHON_PREFIX}/conda-meta/history
 
-if [[ -f /tmp/kernel-environment.yml ]]; then
+if [[ ! -z "${KERNEL_ENVIRONMENT_FILE:-}" && -f "${KERNEL_ENVIRONMENT_FILE}" ]]; then
     # install kernel env and register kernelspec
     echo "installing kernel env:"
-    cat /tmp/kernel-environment.yml
-
-    time mamba create --prefix ${KERNEL_PYTHON_PREFIX} --file /tmp/kernel-environment.yml
+    cat "${KERNEL_ENVIRONMENT_FILE}"
+    if [[ "${KERNEL_ENVIRONMENT_FILE: -5}" == ".lock" ]]; then
+        create="mamba create"
+    else
+        create="mamba env create"
+    fi
+
+    time $create -p ${KERNEL_PYTHON_PREFIX} --file "${KERNEL_ENVIRONMENT_FILE}"
     ${KERNEL_PYTHON_PREFIX}/bin/ipython kernel install --prefix "${NB_PYTHON_PREFIX}"
     echo '' > ${KERNEL_PYTHON_PREFIX}/conda-meta/history
     mamba list -p ${KERNEL_PYTHON_PREFIX}