Rename package to cladetime

.github/workflows/run-code-checks.yaml

@@ -13,14 +13,14 @@ jobs:
 
       - name: Build Docker image 🐳
         run: |
-          docker build -t virus-clade-utils .
+          docker build -t cladetime .
 
       - name: lint 🧹
         run: |
-          docker run --entrypoint /bin/bash virus-clade-utils \
+          docker run --entrypoint /bin/bash cladetime \
           -c "ruff check"
 
       - name: run unit tests 🧪
         run: |
-          docker run --entrypoint /bin/bash virus-clade-utils \
+          docker run --entrypoint /bin/bash cladetime \
           -c "pytest -k unit"

.github/workflows/run-integration-tests.yaml

@@ -15,9 +15,9 @@ jobs:
 
       - name: Build Docker image 🐳
         run: |
-          docker build -t virus-clade-utils .
+          docker build -t cladetime .
 
       - name: run integration tests 🧪
         run: |
-          docker run --entrypoint /bin/bash virus-clade-utils \
+          docker run --entrypoint /bin/bash cladetime \
           -c "pytest -k integration"

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: >
     (?x)(
-        ^src/virus_clade_utils/bin/|
-        ^src/virus_clade_utils/data/
+        ^src/cladetime/bin/|
+        ^src/cladetime/data/
     )
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit

Dockerfile

@@ -10,7 +10,7 @@
 FROM nextstrain/nextclade:3.8.2
 
 FROM python:3.12-slim-bookworm
-COPY --from=0 /usr/bin/nextclade /opt/src/virus_clade_utils/bin/
+COPY --from=0 /usr/bin/nextclade /opt/src/cladetime/bin/
 
 # create a user to run the app
 ARG USERNAME=docker-user
@@ -23,10 +23,10 @@ RUN chown -R docker-user:docker-user /opt/
 ENV PYTHONPATH "${PYTHONPATH}:/opt/"
 
 # Install the dataformat CLI tool
-WORKDIR /opt/src/virus_clade_utils/bin/
+WORKDIR /opt/src/cladetime/bin/
 ADD https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/dataformat ./dataformat
 RUN chmod +x ./dataformat
-ENV PATH "${PATH}:/opt/src/virus_clade_utils/bin/"
+ENV PATH "${PATH}:/opt/src/cladetime/bin/"
 
 # Install Python dependencies
 WORKDIR /opt/
@@ -47,7 +47,7 @@ RUN uv pip install --system polars-lts-cpu --no-cache-dir
 
 USER $USERNAME
 
-COPY src/virus_clade_utils/ ./src/virus_clade_utils/
+COPY src/cladetime/ ./src/cladetime/
 COPY tests/ ./tests/
 
 ENTRYPOINT ["assign_clades"]

README.md

@@ -1,13 +1,13 @@
-# Virus Clade Utils
+# Cladetime
 
-Virus Clade Utils is a wrapper around existing tools for downloading and working with virus genome sequences:
+Cladetime is a wrapper around existing tools for downloading and working with virus genome sequences:
 
 * The [NCBI Datasets API](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/rest-api/) provided by the National Institutes of Healh.
 * The [Nexclade command line interface (CLI)](https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli/index.html) provided by [Nextstrain](https://docs.nextstrain.org/en/latest/).
 
 This package was developed to provide data required for the [COVID-19 Variant Nowcast hub](https://github.com/reichlab/variant-nowcast-hub), where modelers and teams forecast the daily proportions of COVID-19 variants in US states.
 
-We are releasing `virus-clade-utils` as a standalone package for use by others who may find the functionality useful.
+We are releasing `cladetime` as a standalone package for use by others who may find the functionality useful.
 
 
 ## Usage
@@ -24,7 +24,7 @@ This library contains two types of components:
 To use the interactive `CladeTime` object, install this package:
 
 ```bash
-    pip install git+https://github.com/reichlab/virus-clade-utils.git
+    pip install git+https://github.com/reichlab/cladetime.git
 ```
 
 Once the package is installed, you can instantiate a `CladeTime` object in a Python console
@@ -33,7 +33,7 @@ Once the package is installed, you can instantiate a `CladeTime` object in a Pyt
 #### Work with the latest Nextstrain Sars-Cov-2 sequence metadata and clade assignments
 
 ```python
-In [1]: from virus_clade_utils.cladetime import CladeTime
+In [1]: from cladetime.cladetime import CladeTime
 
 In [2]: ct = CladeTime()
 
@@ -86,7 +86,7 @@ Out[9]:
  #### Work with point-in-time Nextstrain Sars-Cov-2 sequence metadata and clade assignments
 
  ```python
-In [10]: from virus_clade_utils.cladetime import CladeTime
+In [10]: from cladetime import CladeTime
 
 In [11]: ct = CladeTime(sequence_as_of="2024-08-31", tree_as_of="2024-08-01")
 
@@ -118,20 +118,20 @@ Use the directions below to run the pipeline in a Docker container.
 1. Clone this repository and change into the high-level directory:
 
     ```bash
-    cd virus-clade-utils
+    cd cladetime
     ```
 2. Build the Docker image:
 
     ```bash
-    docker build --platform=linux/amd64 -t virus-clade-utils .
+    docker build --platform=linux/amd64 -t cladetime .
     ```
 
 3. To run the target data pipeline, passing in required arguments:
 
     ```bash
     docker run --platform linux/amd64 \
     -v $(pwd)/data:/home/docker-user/ \
-    virus-clade-utils \
+    cladetime \
     --sequence-released-since-date 2024-07-16 \
     --reference-tree-date 2024-07-16 \
     --data-dir /home/docker-user
@@ -147,7 +147,7 @@ The clade assignments will now be in the local directory that was mounted to the
 1. Enter the container's bash shell:
 
     ```bash
-    docker run --platform linux/amd64 -it --entrypoint bash virus-clade-utils
+    docker run --platform linux/amd64 -it --entrypoint bash cladetime
     ```
 
 2. Once you're in the shell of the container:
@@ -165,7 +165,7 @@ To run the test suite in the Docker container (built above):
 1. Enter the container's bash shell:
 
     ```bash
-    docker run --platform linux/amd64 -it --entrypoint bash virus-clade-utils
+    docker run --platform linux/amd64 -it --entrypoint bash cladetime
     ```
 
 2. Once you're in the shell of the container, run the tests:
@@ -199,7 +199,7 @@ Follow the directions below to set this project up on your local machine.
 1. Clone this repository and change into the project's high-level directory:
 
     ```bash
-    cd virus-clade-utils
+    cd cladetime
     ```
 
 2. Create a Python virtual environment:

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
-name = "virus-clade-utils"
-version = "0.1.0"
+name = "cladetime"
+version = "0.2.0"
 description = "Assign clades to viral genome sequences at a point in time."
 authors = [
     {name = "Evan Ray", email="[email protected]"},
@@ -43,11 +43,11 @@ dev = [
 ]
 
 [project.urls]
-Repository = "https://github.com/reichlab/virus-clade-utils.git"
+Repository = "https://github.com/reichlab/cladetime.git"
 
 [project.entry-points."console_scripts"]
-assign_clades = "virus_clade_utils.assign_clades:main"
-clade_list = "virus_clade_utils.get_clade_list:main"
+assign_clades = "cladetime.assign_clades:main"
+clade_list = "cladetime.get_clade_list:main"
 
 [build-system]
 requires = ["setuptools>=64", "wheel"]
@@ -68,7 +68,7 @@ line-length = 120
 lint.extend-select = ["I"]
 
 [tools.setuptools]
-packages = ["virus_clade_utils"]
+packages = ["cladetime"]
 
 [tool.mypy]
 ignore_missing_imports = true

requirements/requirements-dev.txt

@@ -1,13 +1,13 @@
 # This file was autogenerated by uv via the following command:
 #    uv pip compile pyproject.toml --extra dev -o requirements/requirements-dev.txt
 awscli==1.32.116
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 boto3==1.34.116
     # via
-    #   virus-clade-utils (pyproject.toml)
+    #   cladetime (pyproject.toml)
     #   moto
 boto3-stubs==1.35.28
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 botocore==1.34.116
     # via
     #   awscli
@@ -24,20 +24,20 @@ charset-normalizer==3.3.2
     # via requests
 click==8.1.7
     # via
-    #   virus-clade-utils (pyproject.toml)
+    #   cladetime (pyproject.toml)
     #   rich-click
 cloudpathlib==0.18.1
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 colorama==0.4.6
     # via awscli
 coverage==7.5.3
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 cryptography==43.0.1
     # via moto
 docutils==0.16
     # via awscli
 freezegun==1.5.1
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 idna==3.7
     # via requests
 iniconfig==2.0.0
@@ -59,9 +59,9 @@ markupsafe==2.1.5
 mdurl==0.1.2
     # via markdown-it-py
 moto==5.0.15
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 mypy==1.10.1
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 mypy-boto3-s3==1.35.22
     # via boto3-stubs
 mypy-extensions==1.0.0
@@ -73,13 +73,13 @@ numpy==1.26.4
 packaging==24.0
     # via pytest
 pandas==2.2.2
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 pluggy==1.5.0
     # via pytest
 polars==1.6.0
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 pyarrow==16.1.0
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 pyasn1==0.6.0
     # via rsa
 pycparser==2.22
@@ -88,10 +88,10 @@ pygments==2.18.0
     # via rich
 pytest==8.2.1
     # via
-    #   virus-clade-utils (pyproject.toml)
+    #   cladetime (pyproject.toml)
     #   pytest-mock
 pytest-mock==3.14.0
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 python-dateutil==2.9.0.post0
     # via
     #   botocore
@@ -106,52 +106,54 @@ pyyaml==6.0.1
     #   responses
 requests==2.32.3
     # via
-    #   virus-clade-utils (pyproject.toml)
+    #   cladetime (pyproject.toml)
     #   moto
     #   responses
 responses==0.25.3
     # via moto
 rich==13.7.1
     # via
-    #   virus-clade-utils (pyproject.toml)
+    #   cladetime (pyproject.toml)
     #   rich-click
 rich-click==1.8.2
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 rsa==4.7.2
     # via awscli
 ruff==0.5.0
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 s3transfer==0.10.1
     # via
     #   awscli
     #   boto3
 six==1.16.0
     # via python-dateutil
 structlog==24.2.0
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 types-awscrt==0.21.5
     # via botocore-stubs
 types-python-dateutil==2.9.0.20240906
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 types-requests==2.32.0.20240914
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 types-s3transfer==0.10.2
     # via boto3-stubs
 typing-extensions==4.12.0
     # via
+    #   boto3-stubs
     #   mypy
+    #   mypy-boto3-s3
     #   rich-click
 tzdata==2024.1
     # via pandas
 urllib3==2.2.1
     # via
-    #   virus-clade-utils (pyproject.toml)
+    #   cladetime (pyproject.toml)
     #   botocore
     #   requests
     #   responses
     #   types-requests
 us==3.2.0
-    # via virus-clade-utils (pyproject.toml)
+    # via cladetime (pyproject.toml)
 werkzeug==3.0.4
     # via moto
 xmltodict==0.13.0