uht-tooling 0.1.2__py3-none-any.whl → 0.1.3__py3-none-any.whl

uht_tooling/cli.py

@@ -18,6 +18,7 @@ from uht_tooling.workflows.umi_hunter import (
     expand_fastq_inputs as expand_fastq_inputs_umi,
     run_umi_hunter,
 )
+from uht_tooling.workflows.gui import launch_gui
 
 app = typer.Typer(help="Command-line interface for the uht-tooling package.")
 
@@ -355,9 +356,34 @@ def profile_inserts_command(
             typer.echo(f"  Sample {entry['sample']}: {entry['directory']}")
 
 
-@app.command("gui", help="Launch the graphical interface (currently under refactor).")
-def gui_command():
-    raise NotImplementedError("The GUI is being updated to work with user-specified data directories.")
+@app.command("gui", help="Launch the graphical interface.")
+def gui_command(
+    server_name: str = typer.Option(
+        "127.0.0.1",
+        "--server-name",
+        "-n",
+        help="Hostname or IP address to bind the GUI server.",
+    ),
+    server_port: Optional[int] = typer.Option(
+        7860,
+        "--server-port",
+        "-p",
+        help="Preferred port for the GUI (falls back automatically if unavailable).",
+    ),
+    share: bool = typer.Option(
+        False,
+        "--share",
+        help="Enable Gradio's public sharing tunnel (requires network access).",
+    ),
+):
+    """Launch the Gradio GUI."""
+    try:
+        launch_gui(server_name=server_name, server_port=server_port, share=share)
+    except KeyboardInterrupt:
+        typer.echo("GUI stopped by user.")
+    except Exception as exc:
+        typer.echo(f"Failed to start GUI: {exc}")
+        raise typer.Exit(1)
 
 
 def main():

{uht_tooling-0.1.2.dist-info → uht_tooling-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: uht-tooling
-Version: 0.1.2
+Version: 0.1.3
 Summary: Tooling for ultra-high throughput screening workflows.
 Author: Matt115A
 License: MIT
@@ -27,7 +27,7 @@ Requires-Dist: ruff==0.14.4; extra == "dev"
 
 # uht-tooling
 
-Automation helpers for ultra-high-throughput molecular biology workflows. The package ships both a Typer-based CLI and an optional Gradio GUI that wrap the same workflow code paths.
+Automation helpers for ultra-high-throughput molecular biology workflows. The package ships both a CLI and an optional GUI that wrap the same workflow code paths.
 
 ---
 
@@ -35,19 +35,20 @@ Automation helpers for ultra-high-throughput molecular biology workflows. The pa
 
 ### Quick install (recommended, easiest file maintainance)
 ```bash
-python -m pip install "uht-tooling[gui]"
+pip install "uht-tooling[gui]==0.1.3"
+
 ```
 
 This installs the core workflows plus the optional GUI dependencies (Gradio, pandas). Omit the `[gui]` extras if you only need the CLI:
 
 ```bash
-python -m pip install uht-tooling
+pip install uht-tooling
 ```
 
 ### Development install
 ```bash
-git clone https://github.com/Matt115A/uht-tooling.git
-cd uht-tooling
+git clone https://github.com/Matt115A/uht-tooling-packaged.git
+cd uht-tooling-packaged
 python -m pip install -e ".[gui,dev]"
 ```
 
@@ -57,7 +58,7 @@ The editable install exposes the latest sources, while the `dev` extras add lint
 
 ## Directory layout
 
-- Reference inputs live under `data/<workflow>/`.
+- Reference inputs can be found anywhere (you specify in the cli), but we recommend using `data/<workflow>/`.
 - Outputs (CSV, FASTA, plots, logs) are written to `results/<workflow>/`.
 - All workflows log to `results/<workflow>/run.log` for reproducibility and debugging.
 
@@ -79,9 +80,9 @@ Each command mirrors a workflow module. Common entry points:
 | `uht-tooling design-slim` | Design SLIM mutagenesis primers from FASTA/CSV inputs. |
 | `uht-tooling design-gibson` | Produce Gibson mutagenesis primers and assembly plans. |
 | `uht-tooling mutation-caller` | Summarise amino-acid substitutions from long-read FASTQ files. |
-| `uht-tooling umi-hunter` | Cluster UMIs and call consensus alleles. |
-| `uht-tooling ep-library-profile` | Measure mutation rates without UMIs. |
-| `uht-tooling profile-inserts` | Extract inserts defined by probe pairs. |
+| `uht-tooling umi-hunter` | Cluster UMIs and call consensus genes. |
+| `uht-tooling ep-library-profile` | Measure mutation rates in plasmid libraries without UMIs. |
+| `uht-tooling profile-inserts` | Extract and analyse inserts defined by flanking probe pairs. |
 
 Each command provides detailed help, including option descriptions and expected file formats:
 
@@ -107,13 +108,13 @@ You can pass multiple FASTQ paths using repeated `--fastq` options or glob patte
    ```
 4. Primer CSVs will be written to `results/nextera_designer/`, accompanied by a log file.
 
-The helper is preloaded with twelve i5 and twelve i7 indices, enabling up to 144 unique amplicons. Downstream lab workflow suggestions (qPCR monitoring, SPRIselect cleanup) remain unchanged from earlier releases.
+The helper is preloaded with twelve i5 and twelve i7 indices, enabling up to 144 unique amplicons.
 
 #### Wet-lab workflow notes
 
 - Perform the initial amplification with an i5/i7 primer pair and monitor a small aliquot by qPCR. Cap thermocycling early so you only generate ~10% of the theoretical yield—this minimizes amplification bias.
 - Purify the product with SPRIselect beads at approximately a 0.65:1 bead:DNA volume ratio to remove residual primers and short fragments.
-- Confirm primer removal using electrophoresis (e.g., BioAnalyzer DNA chip) before moving to sequencing prep.
+- Confirm primer removal and quantify DNA using electrophoresis (e.g., BioAnalyzer DNA chip) before moving to the flow cell.
 
 ### SLIM primer design
 
@@ -158,7 +159,7 @@ Mutation nomenclature examples:
   ```
 - Outputs include primer sets and an assembly-plan CSV.
 
-If mutations fall within overlapping primer windows, design sequential reactions to avoid excessive primer reuse.
+If mutations fall within overlapping primer windows, design sequential reactions. 
 
 ### Mutation caller (no UMIs)
 
@@ -175,7 +176,7 @@ If mutations fall within overlapping primer windows, design sequential reactions
      --output-dir results/mutation_caller/ \
      --threshold 10
    ```
-3. Outputs: per-sample subdirectories with substitution summaries, co-occurrence matrices, and logs.
+3. Outputs: per-sample subdirectories with substitution summaries, co-occurrence matrices, and logs. Co-occurence matrices are experimental and are not yet to be relied on.
 
 ### UMI Hunter
 
@@ -189,6 +190,10 @@ If mutations fall within overlapping primer windows, design sequential reactions
     --output-dir results/umi_hunter/
   ```
 - Tunable parameters include `--umi-identity-threshold` and `--consensus-mutation-threshold`.
+- --umi-identity-threshold is a decimal between 0-1 and defines how similar two UMIs have to be to be considered grouped.
+- --consensus-mutation-threshold is the minimum group size to report a consensus sequence.
+
+Please be aware, this toolkit will not scale well beyond around 50k reads/sample. See UMIC-seq pipelines for efficient UMI-gene dictionary generation.
 
 ### Profile inserts
 
@@ -229,7 +234,7 @@ python -m uht_tooling.workflows.gui
 ```
 
 Key points:
-- The server binds to `http://127.0.0.1:7860` by default and falls back to an available port if 7860 is busy. Copy http://127.0.0.1:7860 into your browser.
+- The server binds to `http://127.0.0.1:7860` by default and falls back to an available port if 7860 is busy. Copy http://127.0.0.1:7860 into your browser to interface with the GUI.
 - Temporary working directories are created under the system temp folder and cleaned automatically.
 - Output archives (ZIP files) mirror the directory structure produced by the CLI.
 

{uht_tooling-0.1.2.dist-info → uht_tooling-0.1.3.dist-info}/RECORD

@@ -1,5 +1,5 @@
 uht_tooling/__init__.py,sha256=hf0tJaa4_9y9aYb8OB1FtJh1FOuX08dQ6_MCveWFNAc,242
-uht_tooling/cli.py,sha256=G8eDBtw_YgcYV7ynk_YD9W2ua0a0pqGCqud5VaHsB6M,11695
+uht_tooling/cli.py,sha256=sQU0duLmMOqvqzB6hDV7GIQYdvzAKKK3rLx0Iq07ZR4,12432
 uht_tooling/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 uht_tooling/workflows/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 uht_tooling/workflows/design_gibson.py,sha256=SQEThq6dxPMPCsUrwqMUaG5I-diE9jUXPRii9Y7O_7U,13617
@@ -10,8 +10,8 @@ uht_tooling/workflows/mutation_caller.py,sha256=BczuNATOSUcmlw-x6qTzEQfW8MBbvGcl
 uht_tooling/workflows/nextera_designer.py,sha256=8MZ_DyQ0JwPojXH5mZ6bAGAkqki_0qQGac45T_Ll8FQ,6170
 uht_tooling/workflows/profile_inserts.py,sha256=C-SZ10YefiV_4QZbo1oEkI4qYipwaYqPP5jF-MC5O58,16947
 uht_tooling/workflows/umi_hunter.py,sha256=kXR7Tw3vK4TnL8OShRt9kZ36ONpOSd-1txwB95Ldi-I,14470
-uht_tooling-0.1.2.dist-info/METADATA,sha256=bu34FtN9RwijcENNhkRxT1LdXQyl8uBfToBOItastDU,10800
-uht_tooling-0.1.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-uht_tooling-0.1.2.dist-info/entry_points.txt,sha256=t3_bMkEnlnV4vd6nrjNQxHDsHzHHoZenhmxuIYLcRBY,53
-uht_tooling-0.1.2.dist-info/top_level.txt,sha256=iTCCiSn0OjrTx1VOdxXhUlPi1TR9LxaJEZJoMyRcv9c,12
-uht_tooling-0.1.2.dist-info/RECORD,,
+uht_tooling-0.1.3.dist-info/METADATA,sha256=0bPz8odnvbX13BvlQC4HsXvJwu7dRK7YyQ2nD7KwHEA,11220
+uht_tooling-0.1.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+uht_tooling-0.1.3.dist-info/entry_points.txt,sha256=t3_bMkEnlnV4vd6nrjNQxHDsHzHHoZenhmxuIYLcRBY,53
+uht_tooling-0.1.3.dist-info/top_level.txt,sha256=iTCCiSn0OjrTx1VOdxXhUlPi1TR9LxaJEZJoMyRcv9c,12
+uht_tooling-0.1.3.dist-info/RECORD,,