Merge pull request #158 from GavinHuttley/develop

DEV: more project rename updates

.github/workflows/release.yml

@@ -52,7 +52,7 @@ jobs:
       - name: Upload sdist and wheel
         uses: actions/upload-artifact@v4
         with:
-          name: elt-wheel-sdist
+          name: eti-wheel-sdist
           path: |
             ./dist/*.whl
             ./dist/*.tar.gz
@@ -69,7 +69,7 @@ jobs:
       - name: Download sdist and wheel
         uses: actions/download-artifact@v4
         with:
-          name: elt-wheel-sdist
+          name: eti-wheel-sdist
           path: ./dist
 
       - name: Publish package distributions to Test PyPI
@@ -89,7 +89,7 @@ jobs:
       - name: Download sdist and wheel
         uses: actions/download-artifact@v4
         with:
-          name: elt-wheel-sdist
+          name: eti-wheel-sdist
           path: ./dist
 
       - name: Publish package distributions to PyPI

.github/workflows/testing_develop.yml

@@ -35,7 +35,7 @@ jobs:
           pip install --upgrade nox
 
       - name: "Run nox for ${{ matrix.python-version }}"
-        run: "nox -s test-${{ matrix.python-version }} -- --cov-report lcov:lcov-${{matrix.os}}-${{matrix.python-version}}.lcov --cov-report term --cov-append --cov ensembl_lite"
+        run: "nox -s test-${{ matrix.python-version }} -- --cov-report lcov:lcov-${{matrix.os}}-${{matrix.python-version}}.lcov --cov-report term --cov-append --cov ensembl_tui"
 
       - name: Coveralls Parallel
         uses: coverallsapp/github-action@v2

README.md

@@ -1,16 +1,26 @@
-[![CI](https://github.com/cogent3/EnsemblLite/actions/workflows/testing_develop.yml/badge.svg)](https://github.com/cogent3/EnsemblLite/actions/workflows/testing_develop.yml)
-[![CodeQL](https://github.com/cogent3/EnsemblLite/actions/workflows/codeql.yml/badge.svg)](https://github.com/cogent3/EnsemblLite/actions/workflows/codeql.yml)
-[![Coverage Status](https://coveralls.io/repos/github/cogent3/EnsemblLite/badge.svg?branch=develop)](https://coveralls.io/github/cogent3/EnsemblLite?branch=develop)
+[![CI](https://github.com/cogent3/ensembl_tui/actions/workflows/testing_develop.yml/badge.svg)](https://github.com/cogent3/ensembl_tui/actions/workflows/testing_develop.yml)
+[![CodeQL](https://github.com/cogent3/ensembl_tui/actions/workflows/codeql.yml/badge.svg)](https://github.com/cogent3/ensembl_tui/actions/workflows/codeql.yml)
+[![Coverage Status](https://coveralls.io/repos/github/cogent3/ensembl_tui/badge.svg?branch=develop)](https://coveralls.io/github/cogent3/ensembl_tui?branch=develop)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
-# EnsemblLite
+# ensembl-tui
 
-EnsemblLite provides the `elt` command line application for obtaining a subset of the data provided by Ensembl which can then be queried locally. You can have multiple such subsets on your machine, each corresponding to a different selection of species and data types.
+ensembl-tui provides the `eti` terminal application for obtaining a subset of the data provided by Ensembl which can then be queried locally. You can have multiple such subsets on your machine, each corresponding to a different selection of species and data types.
 
 > **Warning**
-> EnsemblLite is in a preliminary phase of development with a limited feature set and incomplete test coverage! Please validate results against the web version. If you discover errors, please post a [bug report](https://github.com/cogent3/EnsemblLite/issues).
+> ensembl-tui is in a preliminary phase of development with a limited feature set and incomplete test coverage! Please validate results against the web version. If you discover errors, please post a [bug report](https://github.com/cogent3/ensembl_tui/issues).
 
 ## Installing the software
 
+<details>
+  <summary>General user installation instructions</summary>
+
+  ```
+  $ pip install ensembl-tui
+  ```
+
+</details>
+
 <details>
   <summary>Developer installation instructions</summary>
   Fork the repo and clone your fork to your local machine. In the terminal, create either a python virtual environment or a new conda environment and activate it. In that virtual environment
@@ -26,17 +36,11 @@ EnsemblLite provides the `elt` command line application for obtaining a subset o
   ```
 </details>
 
-<details>
-  <summary>General user installation instructions</summary>
-
-  We have not yet released on pypi. We will provide instructions here for a Docker based installation soon!
-</details>
-
 ## Resources required to subset Ensembl data
 
-Ensembl hosts some very large data sets. You need to have a machine with sufficient disk space to store the data you want to download. At present we do not have support for predicting how much storage would be required for a given selection of species and data types. We advise you to experiment.
+Ensembl hosts some very large data sets. You need to have a machine with sufficient disk space to store the data you want to download. At present we do not have support for predicting how much storage would be required for a given selection of species and data types. You will need to experiment.
 
-Some commands can be run in parallel but have moderate memory requirements. If you have a machine with limited RAM, you may need to reduce the number of parallel processes. Again, we advise you to experiment.
+Some commands can be run in parallel but have moderate memory requirements. If you have a machine with limited RAM, you may need to reduce the number of parallel processes. Again, run some experiments.
 
 ## Getting setup
 
@@ -47,17 +51,17 @@ Some commands can be run in parallel but have moderate memory requirements. If y
 
   <!-- [[[cog
   import cog
-  from ensembl_lite import cli
+  from ensembl_tui import cli
   from click.testing import CliRunner
   runner = CliRunner()
   result = runner.invoke(cli.main, ["exportrc", "--help"])
-  help = result.output.replace("Usage: main", "Usage: elt")
+  help = result.output.replace("Usage: main", "Usage: eti")
   cog.out(
       "```\n{}\n```".format(help)
   )
   ]]] -->
   ```
-  Usage: elt exportrc [OPTIONS]
+  Usage: eti exportrc [OPTIONS]
 
     exports sample config and species table to the nominated path
 
@@ -69,7 +73,7 @@ Some commands can be run in parallel but have moderate memory requirements. If y
   <!-- [[[end]]] -->
 
   ```shell
-  $ elt exportrc -o ~/Desktop/Outbox/ensembl_download
+  $ eti exportrc -o ~/Desktop/Outbox/ensembl_download
   ```
   This command creates a `ensembl_download` download directory and writes two plain text files into it:
 
@@ -85,17 +89,17 @@ Some commands can be run in parallel but have moderate memory requirements. If y
 
   <!-- [[[cog
   import cog
-  from ensembl_lite import cli
+  from ensembl_tui import cli
   from click.testing import CliRunner
   runner = CliRunner()
   result = runner.invoke(cli.main, ["download", "--help"])
-  help = result.output.replace("Usage: main", "Usage: elt")
+  help = result.output.replace("Usage: main", "Usage: eti")
   cog.out(
       "```\n{}\n```".format(help)
   )
   ]]] -->
   ```
-  Usage: elt download [OPTIONS]
+  Usage: eti download [OPTIONS]
 
     download data from Ensembl's ftp site
 
@@ -114,7 +118,7 @@ Some commands can be run in parallel but have moderate memory requirements. If y
 
   ```shell
   $ cd to/directory/with/config.cfg
-  $ elt download -c config.cfg
+  $ eti download -c config.cfg
   ```
 
   > **Note**
@@ -129,17 +133,17 @@ The download creates a new `.cfg` file inside the download directory. This file
 
   <!-- [[[cog
   import cog
-  from ensembl_lite import cli
+  from ensembl_tui import cli
   from click.testing import CliRunner
   runner = CliRunner()
   result = runner.invoke(cli.main, ["install", "--help"])
-  help = result.output.replace("Usage: main", "Usage: elt")
+  help = result.output.replace("Usage: main", "Usage: eti")
   cog.out(
       "```\n{}\n```".format(help)
   )
   ]]] -->
   ```
-  Usage: elt install [OPTIONS]
+  Usage: eti install [OPTIONS]
 
     create the local representations of the data
 
@@ -158,7 +162,7 @@ The following command uses 2 CPUs and has been safe on systems with only 16GB of
 
 ```shell
 $ cd to/directory/with/downloaded_data
-$ elt install -d downloaded_data -np 2
+$ eti install -d downloaded_data -np 2
 ```
 
 </details>
@@ -168,17 +172,17 @@ $ elt install -d downloaded_data -np 2
 
   <!-- [[[cog
   import cog
-  from ensembl_lite import cli
+  from ensembl_tui import cli
   from click.testing import CliRunner
   runner = CliRunner()
   result = runner.invoke(cli.main, ["installed", "--help"])
-  help = result.output.replace("Usage: main", "Usage: elt")
+  help = result.output.replace("Usage: main", "Usage: eti")
   cog.out(
       "```\n{}\n```".format(help)
   )
   ]]] -->
   ```
-  Usage: elt installed [OPTIONS]
+  Usage: eti installed [OPTIONS]
 
     show what is installed
 
@@ -198,21 +202,21 @@ We provide a conventional command line interface for querying the data with subc
 <details>
   <summary>The full list of subcommands</summary>
 
-  You can get help on individual subcommands by running `elt <subcommand>` in the terminal.
+  You can get help on individual subcommands by running `eti <subcommand>` in the terminal.
 
   <!-- [[[cog
   import cog
-  from ensembl_lite import cli
+  from ensembl_tui import cli
   from click.testing import CliRunner
   runner = CliRunner()
   result = runner.invoke(cli.main)
-  help = result.output.replace("Usage: main", "Usage: elt")
+  help = result.output.replace("Usage: main", "Usage: eti")
   cog.out(
       "```\n{}\n```".format(help)
   )
   ]]] -->
   ```
-  Usage: elt [OPTIONS] COMMAND [ARGS]...
+  Usage: eti [OPTIONS] COMMAND [ARGS]...
 
     Tools for obtaining and interrogating subsets of https://ensembl.org genomic
     data.

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["flit_core >=3.2,<4"]
 build-backend = "flit_core.buildapi"
 
 [project]
-name = "ensembl_lite"
+name = "ensembl_tui"
 authors = [
     { name = "Gavin Huttley", email = "[email protected]"},
 ]
@@ -40,20 +40,20 @@ classifiers = [
 dynamic = ["version", "description"]
 
 [project.urls]
-Documentation = "https://github.com/cogent3/EnsemblLite"
-"Bug Tracker" = "https://github.com/cogent3/EnsemblLite/issues"
-"Source Code" = "https://github.com/cogent3/EnsemblLite"
+Documentation = "https://github.com/cogent3/ensembl_tui"
+"Bug Tracker" = "https://github.com/cogent3/ensembl_tui/issues"
+"Source Code" = "https://github.com/cogent3/ensembl_tui"
 
 [project.scripts]
-elt = "ensembl_lite.cli:main"
+eti = "ensembl_tui.cli:main"
 
 [project.optional-dependencies]
 test = [
     "click",
     "pytest",
     "pytest-cov",
     "pytest-xdist",
-    "ruff==0.5.7",
+    "ruff==0.6.3",
     "nox"]
 doc  = ["click==8.1.3",
         "sphinx",
@@ -85,7 +85,7 @@ dev = ["click",
        "pytest",
        "pytest-cov",
        "pytest-xdist",
-       "ruff==0.5.7",
+       "ruff==0.6.3",
        "scriv",
        "sphinx",
        "sphinx-autobuild",
@@ -94,7 +94,7 @@ dev = ["click",
        "sphinxcontrib-bibtex"]
 
 [tool.flit.sdist]
-include = ["src/*", "tests/", "pyproject.toml"]
+include = ["src/*", "tests/*", "pyproject.toml"]
 
 [tool.pytest.ini_options]
 markers = [
@@ -107,7 +107,6 @@ testpaths = "tests"
 
 [tool.ruff]
 exclude = [
-    ".bzr",
     ".direnv",
     ".eggs",
     ".git",
@@ -127,10 +126,8 @@ exclude = [
     ".vscode",
     "__pypackages__",
     "_build",
-    "buck-out",
     "build",
     "dist",
-    "node_modules",
     "site-packages",
     "venv",
 ]
@@ -139,7 +136,7 @@ exclude = [
 line-length = 88
 indent-width = 4
 
-target-version = "py39"
+target-version = "py310"
 
 [tool.ruff.lint]
 # Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
@@ -196,7 +193,7 @@ docstring-code-line-length = "dynamic"
 format="md"
 categories=["Contributors", "ENH", "BUG", "DOC", "Deprecations", "Discontinued"]
 output_file="changelog.md"
-version="literal: src/cogent3/__init__.py:__version__"
+version="literal: src/ensembl_tui/__init__.py:__version__"
 skip_fragments="README.*"
 new_fragment_template="file: changelog.d/templates/new.md.j2"
 entry_title_template="file: changelog.d/templates/title.md.j2"

src/ensembl_lite/_align.py → src/ensembl_tui/_align.py

@@ -9,9 +9,9 @@
 from cogent3.core.alignment import Aligned, Alignment
 from cogent3.core.location import _DEFAULT_GAP_DTYPE, IndelMap
 
-from ensembl_lite import _genome as elt_genome
-from ensembl_lite import _storage_mixin as elt_mixin
-from ensembl_lite import _util as elt_util
+from ensembl_tui import _genome as elt_genome
+from ensembl_tui import _storage_mixin as elt_mixin
+from ensembl_tui import _util as elt_util
 
 _no_gaps = numpy.array([], dtype=_DEFAULT_GAP_DTYPE)
 
@@ -81,7 +81,7 @@ class GapStore(elt_mixin.Hdf5Mixin):
     def __init__(
         self,
         source: elt_util.PathType,
-        align_name: typing.Optional[str] = None,
+        align_name: str | None = None,
         mode: str = "r",
         in_memory: bool = False,
     ):
@@ -402,7 +402,7 @@ def _add_alignments(*alns, sep="?") -> Alignment:
         all_names.update(set(aln.names))
 
     result = {n: [] for n in all_names}
-    for aln, default in zip(alns, defaults):
+    for aln, default in zip(alns, defaults, strict=False):
         data = aln.to_dict()
         for name in all_names:
             result[name].append(data.get(name, default))
@@ -423,7 +423,7 @@ def __init__(
         self,
         align_db: AlignDb,
         genomes: dict[str, elt_genome.Genome],
-        mask_features: typing.Optional[list[str]] = None,
+        mask_features: list[str] | None = None,
         sep: str = "?",
     ) -> None:
         self._align_db = align_db

src/ensembl_lite/_config.py → src/ensembl_tui/_config.py

@@ -1,14 +1,13 @@
 import configparser
 import fnmatch
 import pathlib
-import typing
 from collections.abc import Iterable
 from dataclasses import dataclass
 
 import click
 
-from ensembl_lite import _species as elt_species
-from ensembl_lite import _util as elt_util
+from ensembl_tui import _species as elt_species
+from ensembl_tui import _util as elt_util
 
 INSTALLED_CONFIG_NAME = "installed.cfg"
 DOWNLOADED_CONFIG_NAME = "downloaded.cfg"
@@ -25,7 +24,9 @@ def make_relative_to(
 ) -> pathlib.Path:
     assert staging_path.is_absolute() and install_path.is_absolute()
 
-    for i, (s_part, i_part) in enumerate(zip(staging_path.parts, install_path.parts)):
+    for i, (s_part, i_part) in enumerate(
+        zip(staging_path.parts, install_path.parts, strict=False),
+    ):
         if s_part != i_part:
             break
     change_up = ("..",) * (len(staging_path.parts) - i)
@@ -243,11 +244,11 @@ def _standardise_path(
 
 def read_config(
     config_path: pathlib.Path,
-    root_dir: typing.Optional[pathlib.Path] = None,
+    root_dir: pathlib.Path | None = None,
 ) -> Config:
     """returns ensembl release, local path, and db specifics from the provided
     config path"""
-    from ensembl_lite._download import download_ensembl_tree
+    from ensembl_tui._download import download_ensembl_tree
 
     if not config_path.exists():
         click.secho(f"File not found {config_path.resolve()!s}", fg="red")