Remove CLI (#76)

* Remove code and tests for CLI

* Remove click dependencies

* Remove script entry points

README.md

@@ -196,14 +196,3 @@ Access to historical copies of `ncov_metadata` is what allows Cladetime to
 access past reference trees for custom clade assignments. Cladetime retrieves
 a separate set of `ncov_metadata` for the `tree_as_of` date and uses it to pass
 the correct reference tree to the `assign_clades` method.
-
-## Command line interface (CLI)
-
-Cladetime will also include a command line interface (CLI) for generating
-custom clade assignments without needed to write Python code.
-
-The CLI is not yet implemented, but it will look something like this:
-
-```bash
-assign_clades --sequence-as-of 2024-10-15 --tree-as-of 2024-09-01 --min-collection-date 2024-09-01 --max-collection-date 2024-09-30 --output-file clade_assignments.tsv
-```

pyproject.toml

@@ -20,15 +20,13 @@ dependencies = [
     "awscli>=1.32.92",
     "biopython",
     "boto3",
-    "click",
     "cloudpathlib",
     "docker",
     "pandas",
     "polars>=1.17.1",
     "pyarrow",
     "requests>=2.32.0",
     "rich",
-    "rich-click",
     "structlog",
     "tqdm",
     "urllib3",
@@ -68,10 +66,6 @@ Repository = "https://github.com/reichlab/cladetime.git"
 Documentation = "https://cladetime.readthedocs.io/"
 Issues = "https://github.com/reichlab/cladetime/issues"
 
-[project.entry-points."console_scripts"]
-assign_clades = "cladetime.assign_clades:main"
-clade_list = "cladetime.get_clade_list:main"
-
 [build-system]
 requires = ["setuptools>=64", "wheel"]
 build-backend = "setuptools.build_meta"

requirements/requirements-dev.txt

@@ -24,10 +24,6 @@ cffi==1.17.1
     # via cryptography
 charset-normalizer==3.4.0
     # via requests
-click==8.1.7
-    # via
-    #   cladetime (pyproject.toml)
-    #   rich-click
 cloudpathlib==0.20.0
     # via cladetime (pyproject.toml)
 colorama==0.4.6
@@ -119,10 +115,6 @@ requests==2.32.3
 responses==0.25.3
     # via moto
 rich==13.9.4
-    # via
-    #   cladetime (pyproject.toml)
-    #   rich-click
-rich-click==1.8.3
     # via cladetime (pyproject.toml)
 rsa==4.7.2
     # via awscli
@@ -151,7 +143,6 @@ typing-extensions==4.12.2
     #   boto3-stubs
     #   mypy
     #   mypy-boto3-s3
-    #   rich-click
 tzdata==2024.2
     # via pandas
 urllib3==2.2.3

requirements/requirements.txt

@@ -15,10 +15,6 @@ certifi==2024.8.30
     # via requests
 charset-normalizer==3.4.0
     # via requests
-click==8.1.7
-    # via
-    #   cladetime (pyproject.toml)
-    #   rich-click
 cloudpathlib==0.20.0
     # via cladetime (pyproject.toml)
 colorama==0.4.6
@@ -66,10 +62,6 @@ requests==2.32.3
     #   cladetime (pyproject.toml)
     #   docker
 rich==13.9.4
-    # via
-    #   cladetime (pyproject.toml)
-    #   rich-click
-rich-click==1.8.3
     # via cladetime (pyproject.toml)
 rsa==4.7.2
     # via awscli
@@ -83,8 +75,6 @@ structlog==24.4.0
     # via cladetime (pyproject.toml)
 tqdm==4.67.1
     # via cladetime (pyproject.toml)
-typing-extensions==4.12.2
-    # via rich-click
 tzdata==2024.2
     # via pandas
 urllib3==2.2.3