v1.3.0

.github/workflows/pytest.yml

@@ -1,32 +1,34 @@
-name: CI
+name: pytest
 on:
   push:
     paths:
-      - "bed2idt/**"
+      - "align_trim/**"
       - "tests/**"
       - "pyproject.toml"
-      - "poetry.lock"
+      - "uv.lock"
       - ".github/workflows/pytest.yml"
 
 jobs:
   ci:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
-        poetry-version: ["1.7.1"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         os: [ubuntu-22.04, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+
+      - name: install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: set up python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Run image
-        uses: abatilo/actions-poetry@v2
-        with:
-          poetry-version: ${{ matrix.poetry-version }}
-      - name: Install with poetry
-        run: poetry install --without docs
-      - name: Poetry pytest
-        run: poetry run pytest
+
+      - name: install project
+        run: uv sync --python ${{ matrix.python-version }} --locked --all-extras --dev
+
+      - name: run tests
+        run: uv run --python  ${{ matrix.python-version }} pytest

.pre-commit-config.yaml

@@ -8,9 +8,10 @@ repos:
         args: [--fix, --show-fixes]
       # Run the formatter.
       - id: ruff-format
-  - repo: https://github.com/python-poetry/poetry
-    rev: "1.8.3" # add version here
+
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    # uv version.
+    rev: 0.7.11
     hooks:
-      - id: poetry-check
-      - id: poetry-lock
-      - id: poetry-install
+      - id: uv-lock
+      - id: uv-export

README.md

@@ -10,15 +10,17 @@
 $ pip install bed2idt 
 ```
 
-## Usage
+# CLI
+
+**Usage**:
 
 ```console
 $ bed2idt [OPTIONS] COMMAND [ARGS]...
 ```
 
 **Options**:
 
-* `--version`: Shows the current bed2idt version.
+* `--version`
 * `--install-completion`: Install completion for the current shell.
 * `--show-completion`: Show completion for the current shell, to copy it or customize the installation.
 * `--help`: Show this message and exit.
@@ -42,12 +44,13 @@ $ bed2idt plates [OPTIONS] BEDFILE
 
 **Options**:
 
-* `--output PATH`: The output location of the file. Defaults to output.xlsx  [default: output.xlsx]
-* `--splitby [pool|ref|none]`: Should the primers be split across differant plate  [default: pool]
+* `--output FILE`: The output location of the file. Defaults to output.xlsx  [default: output.xlsx]
+* `--splitby [pool|ref|ref_pool|none]`: Should the primers be split across different plate  [default: pool]
 * `--fillby [rows|cols]`: How should the plate be filled  [default: cols]
 * `--plateprefix TEXT`: The prefix used in naming sheets in the excel file  [default: plate]
 * `--force / --no-force`: Override the output directory
-* `--randomise / --no-randomise`: Randomise the order of primers within a plate
+* `--randomise / --no-randomise`: Randomise the order of primers within a plate  [default: no-randomise]
+* `--platesize [96|384]`: The size of the plate to use  [default: 96]
 * `--help`: Show this message and exit.
 
 ## `bed2idt tubes`
@@ -64,8 +67,9 @@ $ bed2idt tubes [OPTIONS] BEDFILE
 
 **Options**:
 
-* `--output PATH`: The output location of the file. Defaults to output.xlsx  [default: output.xlsx]
-* `--scale [25nm|100nm|250nm|1um|5um|10um]`: The conc of the primers  [default: 25nm]
+* `--output FILE`: The output location of the file. Defaults to output.xlsx  [default: output.xlsx]
+* `--scale [25nm|100nm|250nm|1um|5um|10um]`: The concentration of the primers  [default: 25nm]
 * `--purification [STD|PAGE|HPLC|IEHPLC|RNASE|DUALHPLC|PAGEHPLC]`: The purification of the primers  [default: STD]
 * `--force / --no-force`: Override the output directory
 * `--help`: Show this message and exit.
+

bed2idt/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.2.1"

bed2idt/config.py

@@ -6,9 +6,15 @@
 """
 
 
+class PlateSize(Enum):
+    WELL96 = "96"
+    WELL384 = "384"
+
+
 class PlateSplitBy(Enum):
     POOL = "pool"
     REF = "ref"
+    REF_POOL = "ref_pool"
     NONE = "none"