From 8755b467c1199980e1f2648e01f9f0f02ad84b1d Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Fri, 9 Feb 2018 17:56:48 +0100
Subject: [PATCH 01/12] add assemble_subset

- get_assemble_files() returns list of files needed for assembly
- if buildpack.assemble_with_subset is set, only load assemble_files
  prior to running assembly scripts. Load the rest of the repo afterward

conda opts in to this, but currently I think this works
for everything *except* requirements.txt
---
 repo2docker/buildpacks/conda/__init__.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py
index 8e818bc4d..27446c4d8 100644
--- a/repo2docker/buildpacks/conda/__init__.py
+++ b/repo2docker/buildpacks/conda/__init__.py
@@ -178,6 +178,18 @@ def py2(self):
         """Am I building a Python 2 kernel environment?"""
         return self.python_version and self.python_version.split(".")[0] == "2"
 
+    def get_assemble_files(self):
+        """Specify that assembly only requires environment.yml
+
+        enables caching assembly result even when
+        repo contents change
+        """
+        assemble_files = super().get_assemble_files()
+        environment_yml = self.binder_path('environment.yml')
+        if os.path.exists(environment_yml):
+            assemble_files.append(environment_yml)
+        return assemble_files
+
     def get_assemble_scripts(self):
         """Return series of build-steps specific to this source repository.
         """

From 6ecdbf4ef6f952bba38d4a65c5ca12a21f867a45 Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Tue, 18 Sep 2018 14:42:58 +0200
Subject: [PATCH 02/12] check requirements.txt  for local references

allows assemble_from_subset when requirements.txt doesn't contain any local references
---
 repo2docker/buildpacks/python/__init__.py | 56 +++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/repo2docker/buildpacks/python/__init__.py b/repo2docker/buildpacks/python/__init__.py
index 4db5c72d8..0d9a5b39a 100644
--- a/repo2docker/buildpacks/python/__init__.py
+++ b/repo2docker/buildpacks/python/__init__.py
@@ -34,6 +34,62 @@ def python_version(self):
         self._python_version = py_version
         return self._python_version
 
+    def get_assemble_files(self):
+        assemble_files = super().get_assemble_files()
+        for name in ('requirements.txt', 'requirements3.txt'):
+            requirements_txt = self.binder_path(name)
+            if os.path.exists(requirements_txt):
+                assemble_files.append(requirements_txt)
+        return assemble_files
+
+    def _is_local_requirement(self, line):
+        """Return whether a line in a requirements.txt file references a local file"""
+        # trim comments and skip empty lines
+        line = line.split('#', 1)[0].strip()
+        if not line:
+            return False
+        if line.startswith(('-r', '-c')):
+            # local -r or -c references break isolation
+            return True
+        # strip off `-e, etc.`
+        if line.startswith('-'):
+            line = line.split(None, 1)[1]
+        if 'file://' in line:
+            # file references break isolation
+            return True
+        if '://' in line:
+            # handle git://../local/file
+            path = line.split('://', 1)[1]
+        else:
+            path = line
+        if path.startswith('.'):
+            # references a local file
+            return True
+        return False
+
+    @property
+    def assemble_from_subset(self):
+        """Peek in requirements.txt to determine if we can assemble from only env files
+
+        If there are any local references, e.g. `-e .`,
+        stage the whole repo prior to installation.
+        """
+        if not os.path.exists('binder') and os.path.exists('setup.py'):
+            # can't install from subset if we're using setup.py
+            return False
+        for name in ('requirements.txt', 'requirements3.txt'):
+            requirements_txt = self.binder_path(name)
+            if not os.path.exists(requirements_txt):
+                continue
+            with open(requirements_txt) as f:
+                for line in f:
+                    if self._is_local_requirement(line):
+                        return False
+
+        # didn't find any local references,
+        # allow assembly from subset
+        return True
+
     def get_assemble_scripts(self):
         """Return series of build-steps specific to this repository.
         """

From eb32f84f28ff9fb9a8e494cca702150a23c8f5c0 Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Tue, 16 Jul 2019 08:35:35 +0200
Subject: [PATCH 03/12] move stencila to preassemble

---
 repo2docker/buildpacks/base.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py
index 0bb9703bb..6d77ad273 100644
--- a/repo2docker/buildpacks/base.py
+++ b/repo2docker/buildpacks/base.py
@@ -711,12 +711,8 @@ def get_preassemble_scripts(self):
         except FileNotFoundError:
             pass
 
-        return scripts
-
-    def get_assemble_scripts(self):
-        assemble_scripts = []
         if "py" in self.stencila_contexts:
-            assemble_scripts.extend(
+            scripts.extend(
                 [
                     (
                         "${NB_USER}",
@@ -728,7 +724,7 @@ def get_assemble_scripts(self):
                 ]
             )
         if self.stencila_manifest_dir:
-            assemble_scripts.extend(
+            scripts.extend(
                 [
                     (
                         "${NB_USER}",
@@ -741,7 +737,11 @@ def get_assemble_scripts(self):
                     )
                 ]
             )
-        return assemble_scripts
+        return scripts
+
+    def get_assemble_scripts(self):
+        """Return directives to run after the entire repository has been added to the image"""
+        return []
 
     def get_post_build_scripts(self):
         post_build = self.binder_path("postBuild")

From 9fba04c8710c467dffe2303d0598d8ae0abbdbf1 Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Tue, 16 Jul 2019 08:36:06 +0200
Subject: [PATCH 04/12] conda install occurs in preassemble

---
 repo2docker/buildpacks/conda/__init__.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py
index 27446c4d8..2aa45c37f 100644
--- a/repo2docker/buildpacks/conda/__init__.py
+++ b/repo2docker/buildpacks/conda/__init__.py
@@ -178,19 +178,19 @@ def py2(self):
         """Am I building a Python 2 kernel environment?"""
         return self.python_version and self.python_version.split(".")[0] == "2"
 
-    def get_assemble_files(self):
-        """Specify that assembly only requires environment.yml
+    def get_preassemble_script_files(self):
+        """preassembly only requires environment.yml
 
         enables caching assembly result even when
         repo contents change
         """
-        assemble_files = super().get_assemble_files()
-        environment_yml = self.binder_path('environment.yml')
+        assemble_files = super().get_preassemble_script_files()
+        environment_yml = self.binder_path("environment.yml")
         if os.path.exists(environment_yml):
-            assemble_files.append(environment_yml)
+            assemble_files[environment_yml] = environment_yml
         return assemble_files
 
-    def get_assemble_scripts(self):
+    def get_preassemble_scripts(self):
         """Return series of build-steps specific to this source repository.
         """
         assembly_scripts = []
@@ -209,7 +209,7 @@ def get_assemble_scripts(self):
                     ),
                 )
             )
-        return super().get_assemble_scripts() + assembly_scripts
+        return super().get_preassemble_scripts() + assembly_scripts
 
     def detect(self):
         """Check if current repo should be built with the Conda BuildPack.

From bf45edad335fc8a22397456e3786b7e9f5db9ef1 Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Tue, 16 Jul 2019 09:02:59 +0200
Subject: [PATCH 05/12] preassemble python

---
 repo2docker/buildpacks/python/__init__.py | 110 +++++++++++++---------
 1 file changed, 65 insertions(+), 45 deletions(-)

diff --git a/repo2docker/buildpacks/python/__init__.py b/repo2docker/buildpacks/python/__init__.py
index 0d9a5b39a..7b6fc5afc 100644
--- a/repo2docker/buildpacks/python/__init__.py
+++ b/repo2docker/buildpacks/python/__init__.py
@@ -34,50 +34,79 @@ def python_version(self):
         self._python_version = py_version
         return self._python_version
 
-    def get_assemble_files(self):
-        assemble_files = super().get_assemble_files()
-        for name in ('requirements.txt', 'requirements3.txt'):
-            requirements_txt = self.binder_path(name)
-            if os.path.exists(requirements_txt):
-                assemble_files.append(requirements_txt)
-        return assemble_files
-
     def _is_local_requirement(self, line):
         """Return whether a line in a requirements.txt file references a local file"""
         # trim comments and skip empty lines
-        line = line.split('#', 1)[0].strip()
+        line = line.split("#", 1)[0].strip()
         if not line:
             return False
-        if line.startswith(('-r', '-c')):
+        if line.startswith(("-r", "-c")):
             # local -r or -c references break isolation
             return True
         # strip off `-e, etc.`
-        if line.startswith('-'):
+        if line.startswith("-"):
             line = line.split(None, 1)[1]
-        if 'file://' in line:
+        if "file://" in line:
             # file references break isolation
             return True
-        if '://' in line:
+        if "://" in line:
             # handle git://../local/file
-            path = line.split('://', 1)[1]
+            path = line.split("://", 1)[1]
         else:
             path = line
-        if path.startswith('.'):
+        if path.startswith("."):
             # references a local file
             return True
         return False
 
+    def _get_pip_scripts(self):
+        """Get pip install scripts
+
+        added to preassemble unless local references are found,
+        in which case this happens in assemble.
+        """
+        # KERNEL_PYTHON_PREFIX is the env with the kernel,
+        # whether it's distinct from the notebook or the same.
+        pip = "${KERNEL_PYTHON_PREFIX}/bin/pip"
+        scripts = []
+        if self.py2:
+            # using python 2 kernel,
+            # requirements3.txt allows installation in the notebook server env
+            nb_requirements_file = self.binder_path("requirements3.txt")
+            if os.path.exists(nb_requirements_file):
+                scripts.append(
+                    (
+                        "${NB_USER}",
+                        # want the $NB_PYHTON_PREFIX environment variable, not for
+                        # Python's string formatting to try and replace this
+                        '${{NB_PYTHON_PREFIX}}/bin/pip install --no-cache-dir -r "{}"'.format(
+                            nb_requirements_file
+                        ),
+                    )
+                )
+
+        # install requirements.txt in the kernel env
+        requirements_file = self.binder_path("requirements.txt")
+        if os.path.exists(requirements_file):
+            scripts.append(
+                (
+                    "${NB_USER}",
+                    '{} install --no-cache-dir -r "{}"'.format(pip, requirements_file),
+                )
+            )
+        return scripts
+
     @property
-    def assemble_from_subset(self):
+    def _should_preassemble_pip(self):
         """Peek in requirements.txt to determine if we can assemble from only env files
 
         If there are any local references, e.g. `-e .`,
         stage the whole repo prior to installation.
         """
-        if not os.path.exists('binder') and os.path.exists('setup.py'):
+        if not os.path.exists("binder") and os.path.exists("setup.py"):
             # can't install from subset if we're using setup.py
             return False
-        for name in ('requirements.txt', 'requirements3.txt'):
+        for name in ("requirements.txt", "requirements3.txt"):
             requirements_txt = self.binder_path(name)
             if not os.path.exists(requirements_txt):
                 continue
@@ -90,9 +119,23 @@ def assemble_from_subset(self):
         # allow assembly from subset
         return True
 
+    def get_preassemble_script_files(self):
+        assemble_files = super().get_preassemble_script_files()
+        for name in ("requirements.txt", "requirements3.txt"):
+            requirements_txt = self.binder_path(name)
+            if os.path.exists(requirements_txt):
+                assemble_files[requirements_txt] = requirements_txt
+        return assemble_files
+
+    def get_preassemble_scripts(self):
+        """Return scripts to run before adding the full repository"""
+        scripts = super().get_preassemble_scripts()
+        if self._should_preassemble_pip:
+            scripts.extend(self._get_pip_scripts())
+        return scripts
+
     def get_assemble_scripts(self):
-        """Return series of build-steps specific to this repository.
-        """
+        """Return series of build steps that require the full repository"""
         # If we have a runtime.txt & that's set to python-2.7,
         # requirements.txt will be installed in the *kernel* env
         # and requirements3.txt (if it exists)
@@ -102,31 +145,8 @@ def get_assemble_scripts(self):
         # KERNEL_PYTHON_PREFIX is the env with the kernel,
         # whether it's distinct from the notebook or the same.
         pip = "${KERNEL_PYTHON_PREFIX}/bin/pip"
-        if self.py2:
-            # using python 2 kernel,
-            # requirements3.txt allows installation in the notebook server env
-            nb_requirements_file = self.binder_path("requirements3.txt")
-            if os.path.exists(nb_requirements_file):
-                assemble_scripts.append(
-                    (
-                        "${NB_USER}",
-                        # want the $NB_PYHTON_PREFIX environment variable, not for
-                        # Python's string formatting to try and replace this
-                        '${{NB_PYTHON_PREFIX}}/bin/pip install --no-cache-dir -r "{}"'.format(
-                            nb_requirements_file
-                        ),
-                    )
-                )
-
-        # install requirements.txt in the kernel env
-        requirements_file = self.binder_path("requirements.txt")
-        if os.path.exists(requirements_file):
-            assemble_scripts.append(
-                (
-                    "${NB_USER}",
-                    '{} install --no-cache-dir -r "{}"'.format(pip, requirements_file),
-                )
-            )
+        if not self._should_preassemble_pip:
+            assemble_scripts.extend(self._get_pip_scripts())
 
         # setup.py exists *and* binder dir is not used
         if not self.binder_dir and os.path.exists(setup_py):

From 8227156d91ee60fa387d07c5dfd65e118a0d83d9 Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Tue, 16 Jul 2019 09:11:38 +0200
Subject: [PATCH 06/12] preassembly for pipfiles

---
 repo2docker/buildpacks/pipfile/__init__.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/pipfile/__init__.py b/repo2docker/buildpacks/pipfile/__init__.py
index e91e63aa5..c60a1f881 100644
--- a/repo2docker/buildpacks/pipfile/__init__.py
+++ b/repo2docker/buildpacks/pipfile/__init__.py
@@ -65,7 +65,16 @@ def python_version(self):
             self._python_version = self.major_pythons["3"]
             return self._python_version
 
-    def get_assemble_scripts(self):
+    def get_preassemble_script_files(self):
+        """Return files needed for preassembly"""
+        files = super().get_preassemble_script_files()
+        for name in ("requirements3.txt", "Pipfile", "Pipfile.lock"):
+            path = self.binder_path(name)
+            if os.path.exists(path):
+                files[path] = path
+        return files
+
+    def get_preassemble_scripts(self):
         """Return series of build-steps specific to this repository.
         """
         # If we have either Pipfile.lock, Pipfile, or runtime.txt declare the

From a8703a441bca2417aef47a21e8a4b6b3a9b4cb0c Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Thu, 18 Jul 2019 14:39:35 +0200
Subject: [PATCH 07/12] check for local pip requirements in conda environments

---
 repo2docker/buildpacks/conda/__init__.py  | 104 +++++++++++++++-------
 repo2docker/buildpacks/python/__init__.py |  28 +-----
 repo2docker/utils.py                      |  26 ++++++
 3 files changed, 102 insertions(+), 56 deletions(-)

diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py
index 2aa45c37f..87865250e 100644
--- a/repo2docker/buildpacks/conda/__init__.py
+++ b/repo2docker/buildpacks/conda/__init__.py
@@ -6,6 +6,7 @@
 from ruamel.yaml import YAML
 
 from ..base import BaseImage
+from ...utils import is_local_pip_requirement
 
 # pattern for parsing conda dependency line
 PYTHON_REGEX = re.compile(r"python\s*=+\s*([\d\.]*)")
@@ -127,6 +128,50 @@ def get_build_script_files(self):
         files.update(super().get_build_script_files())
         return files
 
+    _environment_yaml = None
+
+    @property
+    def environment_yaml(self):
+        if self._environment_yaml is not None:
+            return self._environment_yaml
+
+        environment_yml = self.binder_path("environment.yml")
+        if not os.path.exists(environment_yml):
+            self._environment_yaml = {}
+            return self._environment_yaml
+
+        with open(environment_yml) as f:
+            env = YAML().load(f)
+            # check if the env file is empty, if so instantiate an empty dictionary.
+            if env is None:
+                env = {}
+            # check if the env file provided a dick-like thing not a list or other data structure.
+            if not isinstance(env, Mapping):
+                raise TypeError(
+                    "environment.yml should contain a dictionary. Got %r" % type(env)
+                )
+            self._environment_yaml = env
+
+        return self._environment_yaml
+
+    @property
+    def _should_preassemble_env(self):
+        """Check for local pip requirements in environment.yaml
+
+        If there are any local references, e.g. `-e .`,
+        stage the whole repo prior to installation.
+        """
+        dependencies = self.environment_yaml.get("dependencies", [])
+        pip_requirements = None
+        for dep in dependencies:
+            if isinstance(dep, dict) and dep.get("pip"):
+                pip_requirements = dep["pip"]
+        if isinstance(pip_requirements, list):
+            for line in pip_requirements:
+                if is_local_pip_requirement(line):
+                    return False
+        return True
+
     @property
     def python_version(self):
         """Detect the Python version for a given `environment.yml`
@@ -135,31 +180,17 @@ def python_version(self):
         or a Falsy empty string '' if not found.
 
         """
-        environment_yml = self.binder_path("environment.yml")
-        if not os.path.exists(environment_yml):
-            return ""
-
         if not hasattr(self, "_python_version"):
             py_version = None
-            with open(environment_yml) as f:
-                env = YAML().load(f)
-                # check if the env file is empty, if so instantiate an empty dictionary.
-                if env is None:
-                    env = {}
-                # check if the env file provided a dick-like thing not a list or other data structure.
-                if not isinstance(env, Mapping):
-                    raise TypeError(
-                        "environment.yml should contain a dictionary. Got %r"
-                        % type(env)
-                    )
-                for dep in env.get("dependencies", []):
-                    if not isinstance(dep, str):
-                        continue
-                    match = PYTHON_REGEX.match(dep)
-                    if not match:
-                        continue
-                    py_version = match.group(1)
-                    break
+            env = self.environment_yaml
+            for dep in env.get("dependencies", []):
+                if not isinstance(dep, str):
+                    continue
+                match = PYTHON_REGEX.match(dep)
+                if not match:
+                    continue
+                py_version = match.group(1)
+                break
 
             # extract major.minor
             if py_version:
@@ -185,19 +216,20 @@ def get_preassemble_script_files(self):
         repo contents change
         """
         assemble_files = super().get_preassemble_script_files()
-        environment_yml = self.binder_path("environment.yml")
-        if os.path.exists(environment_yml):
-            assemble_files[environment_yml] = environment_yml
+        if self._should_preassemble_env:
+            environment_yml = self.binder_path("environment.yml")
+            if os.path.exists(environment_yml):
+                assemble_files[environment_yml] = environment_yml
         return assemble_files
 
-    def get_preassemble_scripts(self):
+    def get_env_scripts(self):
         """Return series of build-steps specific to this source repository.
         """
-        assembly_scripts = []
+        scripts = []
         environment_yml = self.binder_path("environment.yml")
         env_prefix = "${KERNEL_PYTHON_PREFIX}" if self.py2 else "${NB_PYTHON_PREFIX}"
         if os.path.exists(environment_yml):
-            assembly_scripts.append(
+            scripts.append(
                 (
                     "${NB_USER}",
                     r"""
@@ -209,7 +241,19 @@ def get_preassemble_scripts(self):
                     ),
                 )
             )
-        return super().get_preassemble_scripts() + assembly_scripts
+        return scripts
+
+    def get_preassemble_scripts(self):
+        scripts = super().get_preassemble_scripts()
+        if self._should_preassemble_env:
+            scripts.extend(self.get_env_scripts())
+        return scripts
+
+    def get_assemble_scripts(self):
+        scripts = super().get_assemble_scripts()
+        if not self._should_preassemble_env:
+            scripts.extend(self.get_env_scripts())
+        return scripts
 
     def detect(self):
         """Check if current repo should be built with the Conda BuildPack.
diff --git a/repo2docker/buildpacks/python/__init__.py b/repo2docker/buildpacks/python/__init__.py
index 7b6fc5afc..72029d78b 100644
--- a/repo2docker/buildpacks/python/__init__.py
+++ b/repo2docker/buildpacks/python/__init__.py
@@ -2,6 +2,7 @@
 import os
 
 from ..conda import CondaBuildPack
+from ...utils import is_local_pip_requirement
 
 
 class PythonBuildPack(CondaBuildPack):
@@ -34,31 +35,6 @@ def python_version(self):
         self._python_version = py_version
         return self._python_version
 
-    def _is_local_requirement(self, line):
-        """Return whether a line in a requirements.txt file references a local file"""
-        # trim comments and skip empty lines
-        line = line.split("#", 1)[0].strip()
-        if not line:
-            return False
-        if line.startswith(("-r", "-c")):
-            # local -r or -c references break isolation
-            return True
-        # strip off `-e, etc.`
-        if line.startswith("-"):
-            line = line.split(None, 1)[1]
-        if "file://" in line:
-            # file references break isolation
-            return True
-        if "://" in line:
-            # handle git://../local/file
-            path = line.split("://", 1)[1]
-        else:
-            path = line
-        if path.startswith("."):
-            # references a local file
-            return True
-        return False
-
     def _get_pip_scripts(self):
         """Get pip install scripts
 
@@ -112,7 +88,7 @@ def _should_preassemble_pip(self):
                 continue
             with open(requirements_txt) as f:
                 for line in f:
-                    if self._is_local_requirement(line):
+                    if is_local_pip_requirement(line):
                         return False
 
         # didn't find any local references,
diff --git a/repo2docker/utils.py b/repo2docker/utils.py
index a53ba5ef1..1c0a43341 100644
--- a/repo2docker/utils.py
+++ b/repo2docker/utils.py
@@ -431,3 +431,29 @@ def normalize_doi(val):
     (e.g. https://doi.org/10.1234/jshd123)"""
     m = doi_regexp.match(val)
     return m.group(2)
+
+
+def is_local_pip_requirement(line):
+    """Return whether a pip requirement (e.g. in requirements.txt file) references a local file"""
+    # trim comments and skip empty lines
+    line = line.split("#", 1)[0].strip()
+    if not line:
+        return False
+    if line.startswith(("-r", "-c")):
+        # local -r or -c references break isolation
+        return True
+    # strip off `-e, etc.`
+    if line.startswith("-"):
+        line = line.split(None, 1)[1]
+    if "file://" in line:
+        # file references break isolation
+        return True
+    if "://" in line:
+        # handle git://../local/file
+        path = line.split("://", 1)[1]
+    else:
+        path = line
+    if path.startswith("."):
+        # references a local file
+        return True
+    return False

From edf14b646f9ebd88d643bec1ae2ee3a29e124cf2 Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Thu, 18 Jul 2019 14:40:08 +0200
Subject: [PATCH 08/12] set permissions on repo_dir prior to preassemble

---
 repo2docker/buildpacks/base.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py
index 6d77ad273..b2772e9ef 100644
--- a/repo2docker/buildpacks/base.py
+++ b/repo2docker/buildpacks/base.py
@@ -132,6 +132,10 @@
 {% endfor -%}
 {% endif -%}
 
+{% if preassemble_script_directives -%}
+RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR}
+{% endif -%}
+
 {% for sd in preassemble_script_directives -%}
 {{ sd }}
 {% endfor %}

From 65e3fec4c48a5a7eeea977de3ea78705f88d495f Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Thu, 18 Jul 2019 14:40:17 +0200
Subject: [PATCH 09/12] test local pip requirements

---
 tests/unit/test_utils.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/tests/unit/test_utils.py b/tests/unit/test_utils.py
index 6ad1ff281..951f2085d 100644
--- a/tests/unit/test_utils.py
+++ b/tests/unit/test_utils.py
@@ -110,3 +110,20 @@ def test_normalize_doi():
     assert utils.normalize_doi("http://doi.org/10.1234/jshd123") == "10.1234/jshd123"
     assert utils.normalize_doi("https://doi.org/10.1234/jshd123") == "10.1234/jshd123"
     assert utils.normalize_doi("http://dx.doi.org/10.1234/jshd123") == "10.1234/jshd123"
+
+
+@pytest.mark.parametrize(
+    "req, is_local",
+    [
+        ("-r requirements.txt", True),
+        ("-e .", True),
+        ("file://subdir", True),
+        ("file://./subdir", True),
+        ("git://github.com/jupyter/repo2docker", False),
+        ("git+https://github.com/jupyter/repo2docker", False),
+        ("numpy", False),
+        ("# -e .", False),
+    ],
+)
+def test_local_pip_requirement(req, is_local):
+    assert utils.is_local_pip_requirement(req) == is_local

From 909643972b6d8999a2e57724e9ed42e03a26ba7c Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Thu, 18 Jul 2019 16:25:04 +0200
Subject: [PATCH 10/12] only install pipenv in preassemble

save preassembly of pipenv for a later patch
---
 repo2docker/buildpacks/pipfile/__init__.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/repo2docker/buildpacks/pipfile/__init__.py b/repo2docker/buildpacks/pipfile/__init__.py
index c60a1f881..b38db08a8 100644
--- a/repo2docker/buildpacks/pipfile/__init__.py
+++ b/repo2docker/buildpacks/pipfile/__init__.py
@@ -75,6 +75,15 @@ def get_preassemble_script_files(self):
         return files
 
     def get_preassemble_scripts(self):
+        """scripts to run prior to staging the repo contents"""
+        scripts = super().get_preassemble_scripts()
+        # install pipenv to install dependencies within Pipfile.lock or Pipfile
+        scripts.append(
+            ("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/bin/pip install pipenv==2018.11.26")
+        )
+        return scripts
+
+    def get_assemble_scripts(self):
         """Return series of build-steps specific to this repository.
         """
         # If we have either Pipfile.lock, Pipfile, or runtime.txt declare the
@@ -113,11 +122,6 @@ def get_preassemble_scripts(self):
         #     my_package_example = {path=".", editable=true}
         working_directory = self.binder_dir or "."
 
-        # install pipenv to install dependencies within Pipfile.lock or Pipfile
-        assemble_scripts.append(
-            ("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/bin/pip install pipenv==2018.11.26")
-        )
-
         # NOTES:
         # - Without prioritizing the PATH to KERNEL_PYTHON_PREFIX over
         #   NB_SERVER_PYTHON_PREFIX, 'pipenv' draws the wrong conclusion about

From 7d439efa7aa1e3c26650cc5dab681d08531fce98 Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Thu, 18 Jul 2019 17:55:38 +0200
Subject: [PATCH 11/12] run chown as root

---
 repo2docker/buildpacks/base.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py
index b2772e9ef..140a1d331 100644
--- a/repo2docker/buildpacks/base.py
+++ b/repo2docker/buildpacks/base.py
@@ -133,6 +133,7 @@
 {% endif -%}
 
 {% if preassemble_script_directives -%}
+USER root
 RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR}
 {% endif -%}
 

From 3aa7e39c1be98f8c44748621fbdcebc1fb877143 Mon Sep 17 00:00:00 2001
From: Min RK <benjaminrk@gmail.com>
Date: Fri, 19 Jul 2019 08:56:06 +0200
Subject: [PATCH 12/12] Update repo2docker/buildpacks/conda/__init__.py

Co-Authored-By: Tim Head <betatim@gmail.com>
---
 repo2docker/buildpacks/conda/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py
index 87865250e..c781f00a0 100644
--- a/repo2docker/buildpacks/conda/__init__.py
+++ b/repo2docker/buildpacks/conda/__init__.py
@@ -145,7 +145,7 @@ def environment_yaml(self):
             # check if the env file is empty, if so instantiate an empty dictionary.
             if env is None:
                 env = {}
-            # check if the env file provided a dick-like thing not a list or other data structure.
+            # check if the env file provided a dict-like thing not a list or other data structure.
             if not isinstance(env, Mapping):
                 raise TypeError(
                     "environment.yml should contain a dictionary. Got %r" % type(env)