Merge pull request #64 from paxtonfitzpatrick/main

final tweaks to code, tests, paper draft

Author: paxtonfitzpatrick

.github/workflows/ci-tests-jupyter.yml

@@ -42,13 +42,13 @@ jobs:
           - python-version: 3.7
             ipython-version: 5.5.0    # earliest version supported by davos
           - python-version: 3.7
-            ipython-version: latest
+            ipython-version: 7.31     # latest version to support Python 3.7
           - python-version: 3.8
-            ipython-version: 7.3.0     # earliest version to support Python 3.8
+            ipython-version: 7.3.0    # earliest version to support Python 3.8
           - python-version: 3.8
             ipython-version: latest
           - python-version: 3.9
-            ipython-version: 7.15      # earliest version to support Python 3.9
+            ipython-version: 7.15     # earliest version to support Python 3.9
           - python-version: 3.9
             ipython-version: latest
     env:
@@ -111,7 +111,7 @@ jobs:
           if [[ "$PYTHON_VERSION" =~ ^3.(6|7)$ ]]; then
               pip install typing-extensions
           fi
-          [[ "$PYTHON_VERSION" == "3.6" ]] || pip install numpy==1.20.3
+          [[ "$PYTHON_VERSION" == "3.6" ]] || pip install numpy==1.20.3	
           pip install "ipykernel==5.0.0" ipython-genutils requests scipy fastdtw==0.3.4 tqdm==4.41.1
           if [[ "$IPYTHON_VERSION" == "latest" ]]; then
               pip install --upgrade IPython

davos/core/core.py

@@ -854,7 +854,7 @@ def smuggle(
         install_pkg = True
 
     if install_pkg:
-        # TODO: check for --yes (conda) and bypass if passed
+        # TODO: for v0.2 conda implementation: bypass if -y/--yes passed
         if config.confirm_install and not installer_kwargs.get('no_input'):
             msg = (f"package '{pkg_name}' will be installed with the "
                    f"following command:\n\t`{onion.install_cmd}`\n"

davos/core/parsers.py

@@ -453,7 +453,7 @@ def __call__(self, parser, namespace, values, option_string=None):
     action='store_true',
     help="Do not warn about broken dependencies"
 )
-# NOTE: in the actual pip-install implementation, `--no-binary`,
+# note: in the actual pip-install implementation, `--no-binary`,
 #  `--only-binary`, and `--prefer-binary` triggers a fairly complex
 #  callback. But fortunately, we can just store all invocations and
 #  forward them to the real pip-install parser

davos/implementations/jupyter.py

@@ -14,7 +14,6 @@
 import ipykernel
 import zmq
 from IPython.display import display, Javascript
-from ipython_genutils import py3compat
 
 from davos import config
 from davos.implementations.js_functions import JS_FUNCTIONS
@@ -132,7 +131,7 @@ def prompt_restart_rerun_buttons(pkgs):
        in notebook environments.
 
     """
-    # TODO: remove warning message when button is clicked
+    # UI: could remove warning message when "continue" button is clicked
     msg = (
         "WARNING: The following packages were previously imported by the "
         "interpreter and could not be reloaded because their compiled modules "
@@ -213,7 +212,7 @@ def prompt_restart_rerun_buttons(pkgs):
 
     # noinspection PyBroadException
     try:
-        value = py3compat.unicode_to_str(reply['content']['value'])
+        value = reply['content']['value']
     except Exception:    # pylint: disable=broad-except
         if ipykernel.version_info[0] >= 6:
             _parent_header = kernel._parent_ident['shell']

paper/paper.md

@@ -127,16 +127,16 @@ Google Colaboratory], community-maintained libraries for data manipulation
 visualization [e.g., `Matplotlib`, @Hunt07; `seaborn`, @Wask21], and myriad
 other tools.
 
-However, one impediment to sharing and reproducing computational work
-implemented in Python is that different versions of a given package or library
-can behave differently, use different syntax, add or drop support for specific
-functions or other libraries, address (or introduce) bugs, and so on. While
-these challenges are present to some extent in any language or ecosystem, they
-have a particular impact on the Python community due to its unusually rapid
-growth relative to other languages. Ensuring stable and reproducible results
-across users typically requires ensuring that shared code is always run with the
-same set of versions for each package used. One common approach to solving this
-problem is to create containerized or virtualized environments (e.g., using
+One impediment to sharing and reproducing computational work implemented in
+Python is that different versions of a given package or library can behave
+differently, use different syntax, add or drop support for specific functions or
+other libraries, address (or introduce) bugs, and so on. While these challenges
+are present to some extent in any language or ecosystem, they have a particular
+impact on the Python community due to its unusually rapid growth relative to
+other languages. Ensuring stable and reproducible results across users typically
+requires ensuring that shared code is always run with the same set of versions
+for each package used. One common approach to solving this problem is to create
+containerized or virtualized environments (e.g., using
 [Docker](https://www.docker.com/),
 [Singularity](https://sylabs.io/singularity/), or
 [conda](https://docs.conda.io/en/latest/)) that house fully isolated Python
@@ -171,7 +171,7 @@ are satisfied after they are initially installed. Most dependency specification
 schemes follow a common strategy: required packages and package versions are
 listed in a configuration file (e.g., a `requirements.txt`, `pyproject.toml`,
 `environment.yml`, `Pipfile`, `RUN` instructions in a `Dockerfile`, etc.) which
-is used to install them in a Python environment upfront. After this initial
+is used to install them in a Python environment up front. After this initial
 setup, however, this method generally does not ensure that the specified
 requirements *remain* installed, allowing them to be easily
 altered—sometimes inadvertently. This can lead to subtle issues when

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = davos
-version = 0.0.1
+version = 0.1.0
 description = Install and manage Python packages at runtime using the "smuggle" statement.
 long_description = file: README.md
 long_description_content_type = text/markdown

tests/conftest.py

@@ -58,7 +58,7 @@
     'xpath'
 ]
 _E = TypeVar('_E', bound=BaseException)
-_IpyVersions = Literal['5.5.0', '7.3.0', '7.15', '7.16', 'latest']
+_IpyVersions = Literal['5.5.0', '7.3.0', '7.15', '7.16', '7.31', 'latest']
 _NbTypes = Literal['colab', 'jupyter']
 _PyVersions = Literal['3.6', '3.7', '3.8', '3.9']
 
@@ -569,7 +569,6 @@ def collect(self) -> Iterator[NotebookTest]:
                     yield test_obj
 
     def setup(self) -> None:
-        # TODO: refactor this to call self.driver.<setup_func>()?
         super().setup()
         self.driver = self.driver_cls(self.notebook_path)
         self.driver.clear_all_outputs()