Merge pull request #43 from sanjaynagi/change-name-anoprimer

Change package name to AnoPrimer

.github/workflows/github-action-AgamPrimer-funestus.yml

@@ -35,10 +35,10 @@ jobs:
     - name: Install dependencies
       run: |
         poetry install
-        poetry run python -m ipykernel install --user --name AgamPrimer
+        poetry run python -m ipykernel install --user --name AnoPrimer
 
     - name: Run notebooks
       run: |
-        poetry run papermill notebooks/AgamPrimer-long.ipynb qPCR_run.ipynb -k AgamPrimer -f tests/cDNA_Params_fun.json
-        poetry run papermill notebooks/AgamPrimer-long.ipynb qPCR2_run.ipynb -k AgamPrimer -f tests/cDNA_Params_2_fun.json
-        poetry run papermill notebooks/AgamPrimer-long.ipynb gDNA_run.ipynb -k AgamPrimer -f tests/gDNA_probe_Params_fun.json
+        poetry run papermill notebooks/AnoPrimer-long.ipynb qPCR_run.ipynb -k AnoPrimer -f tests/cDNA_Params_fun.json
+        poetry run papermill notebooks/AnoPrimer-long.ipynb qPCR2_run.ipynb -k AnoPrimer -f tests/cDNA_Params_2_fun.json
+        poetry run papermill notebooks/AnoPrimer-long.ipynb gDNA_run.ipynb -k AnoPrimer -f tests/gDNA_probe_Params_fun.json

.github/workflows/github-action-AgamPrimer-gambiae.yml

@@ -35,12 +35,12 @@ jobs:
     - name: Install dependencies
       run: |
         poetry install
-        poetry run python -m ipykernel install --user --name AgamPrimer
+        poetry run python -m ipykernel install --user --name AnoPrimer
 
     - name: Run notebooks
       run: |
-        poetry run papermill notebooks/AgamPrimer-long.ipynb qPCR_run.ipynb -k AgamPrimer -f tests/cDNA_Params.json
-        poetry run papermill notebooks/AgamPrimer-long.ipynb qPCR2_run.ipynb -k AgamPrimer -f tests/cDNA_Params_2.json
-        poetry run papermill notebooks/AgamPrimer-long.ipynb gDNA_run.ipynb -k AgamPrimer -f tests/gDNA_probe_Params.json
-        poetry run papermill notebooks/AgamPrimer-long.ipynb probe_run.ipynb -k AgamPrimer -f tests/probe_Params.json
-        poetry run papermill notebooks/AgamPrimer-short.ipynb short_run.ipynb -k AgamPrimer
+        poetry run papermill notebooks/AnoPrimer-long.ipynb qPCR_run.ipynb -k AnoPrimer -f tests/cDNA_Params.json
+        poetry run papermill notebooks/AnoPrimer-long.ipynb qPCR2_run.ipynb -k AnoPrimer -f tests/cDNA_Params_2.json
+        poetry run papermill notebooks/AnoPrimer-long.ipynb gDNA_run.ipynb -k AnoPrimer -f tests/gDNA_probe_Params.json
+        poetry run papermill notebooks/AnoPrimer-long.ipynb probe_run.ipynb -k AnoPrimer -f tests/probe_Params.json
+        poetry run papermill notebooks/AnoPrimer-short.ipynb short_run.ipynb -k AnoPrimer

.github/workflows/release.yml

@@ -0,0 +1,31 @@
+name: release
+on:
+    push:
+        tags:
+            - 'v*.*.*'
+jobs:
+    build:
+        runs-on: ubuntu-latest
+        steps:
+            - name: Checkout source
+              uses: actions/checkout@v3
+
+            - name: Install poetry
+              run: pipx install poetry==1.7.1
+
+            - name: Setup python
+              uses: actions/setup-python@v4
+              with:
+                  python-version: '3.10'
+                  cache: 'poetry'
+
+            - name: Configure poetry
+              run: |
+                poetry self add "poetry-dynamic-versioning[plugin]"
+                poetry config pypi-token.pypi ${{ secrets.PYPI_API_TOKEN }}
+
+            - name: Build package
+              run: poetry build
+
+            - name: Publish to PyPI
+              run: poetry publish

AgamPrimer/AgamPrimer.py → AnoPrimer/AnoPrimer.py

@@ -698,7 +698,7 @@ def designPrimers(
     cDNA_exon_junction=True,
 ):
     """
-    Run whole AgamPrimer workflow to design primers/probes with in one function
+    Run whole AnoPrimer workflow to design primers/probes with in one function
 
     Parameters
     ----------
@@ -799,7 +799,7 @@ def designPrimers(
             print(primer3_run_statistics(primer_dict, assay_type))
             return (None, None)
 
-    # AgamPrimer.primer3_run_statistics(primer_dict, assay_type)
+    # AnoPrimer.primer3_run_statistics(primer_dict, assay_type)
     primer_df = primer3_to_pandas(primer_dict=primer_dict, assay_type=assay_type)
 
     # plot frequencies of alleles in primer pairs

AnoPrimer/__init__.py

@@ -0,0 +1,3 @@
+# flake8: noqa
+from . import AnoPrimer
+from .AnoPrimer import *

README.md

@@ -1,10 +1,10 @@
 <div align="center">
 
-[<img src="https://github.com/sanjaynagi/AgamPrimer/blob/main/graphics/AgamPrimer_logo.png?raw=True" width="400"/>](https://github.com/sanjaynagi/AgamPrimer/blob/main/graphics/AgamPrimer_logo.png?raw=True)
+[<img src="https://github.com/sanjaynagi/AnoPrimer/blob/main/graphics/AnoPrimer_logo.png?raw=True" width="400"/>](https://github.com/sanjaynagi/AnoPrimer/blob/main/graphics/AnoPrimer_logo.png?raw=True)
 
 [![DOI](https://zenodo.org/badge/503315581.svg)](https://zenodo.org/badge/latestdoi/503315581)
-[![Execute notebooks](https://github.com/sanjaynagi/AgamPrimer/workflows/Execute%20notebooks/badge.svg)](https://github.com/sanjaynagi/AgamPrimer/actions?query=workflow:"Execute+notebook")
-[![GitHub release](https://img.shields.io/github/release/sanjaynagi/AgamPrimer?include_prereleases=&sort=semver&color=blue)](https://github.com/sanjaynagi/AgamPrimer/releases/)
+[![Execute notebooks](https://github.com/sanjaynagi/AnoPrimer/workflows/Execute%20notebooks/badge.svg)](https://github.com/sanjaynagi/AnoPrimer/actions?query=workflow:"Execute+notebook")
+[![GitHub release](https://img.shields.io/github/release/sanjaynagi/AnoPrimer?include_prereleases=&sort=semver&color=blue)](https://github.com/sanjaynagi/AnoPrimer/releases/)
 [![License](https://img.shields.io/badge/License-MIT-blue)](#license)
 [![Twitter Follow](https://img.shields.io/twitter/follow/sanjay_c_nagi.svg?style=social)](https://twitter.com/sanjay_c_nagi)
 
@@ -14,11 +14,11 @@ Primer design in *Anopheles gambiae s.l* taking into account SNP variation in pr
 <br/><br/>
 <div align="center">
 
-Documentation: https://sanjaynagi.github.io/AgamPrimer/
+Documentation: https://sanjaynagi.github.io/AnoPrimer/
 
-[![Custom badge](https://img.shields.io/endpoint?color=white&logo=Google%20Colab&url=https%3A%2F%2Fraw.githubusercontent.com%2Fsanjaynagi%2FAgamPrimer%2Fmain%2Fgraphics%2Fbadge.json)](https://colab.research.google.com/github/sanjaynagi/AgamPrimer/blob/main/notebooks/AgamPrimer-long.ipynb)
+[![Custom badge](https://img.shields.io/endpoint?color=white&logo=Google%20Colab&url=https%3A%2F%2Fraw.githubusercontent.com%2Fsanjaynagi%2FAnoPrimer%2Fmain%2Fgraphics%2Fbadge.json)](https://colab.research.google.com/github/sanjaynagi/AnoPrimer/blob/main/notebooks/AnoPrimer-long.ipynb)
 
- [![Custom badge](https://img.shields.io/endpoint?color=red&logo=Google%20Colab&url=https%3A%2F%2Fraw.githubusercontent.com%2Fsanjaynagi%2FAgamPrimer%2Fmain%2Fgraphics%2Fbadge-short.json)](https://colab.research.google.com/github/sanjaynagi/AgamPrimer/blob/main/notebooks/AgamPrimer-short.ipynb)
+ [![Custom badge](https://img.shields.io/endpoint?color=red&logo=Google%20Colab&url=https%3A%2F%2Fraw.githubusercontent.com%2Fsanjaynagi%2FAnoPrimer%2Fmain%2Fgraphics%2Fbadge-short.json)](https://colab.research.google.com/github/sanjaynagi/AnoPrimer/blob/main/notebooks/AnoPrimer-short.ipynb)
 
 </div>
 

docs/AgamPrimer-docs/_config.yml → docs/AnoPrimer-docs/_config.yml

@@ -13,7 +13,7 @@ execute:
 
 # Information about where the book exists on the web
 repository:
-  url: https://github.com/sanjaynagi.github.io/AgamPrimer # Online location of your book
+  url: https://github.com/sanjaynagi.github.io/AnoPrimer # Online location of your book
   path_to_book: docs/  # Optional path to your book, relative to the repository root
   branch: main  # Which branch of the repository should be used when creating links (optional)
 
@@ -29,7 +29,7 @@ sphinx:
 # Define the name of the latex output file for PDF builds
 latex:
   latex_documents:
-    targetname: AgamPrimer.tex
+    targetname: AnoPrimer.tex
 
 # Add a bibtex file so that we can create citations
 #bibtex_bibfiles:
@@ -42,7 +42,7 @@ html:
   use_repository_button: true
   comments:
     utterances:
-      repo: "sanjaynagi/AgamPrimer"
+      repo: "sanjaynagi/AnoPrimer"
       issue-term: "pathname"
       label: "comment"
       theme: "github-light"

docs/AnoPrimer-docs/landing-page.md

@@ -0,0 +1,9 @@
+# AnoPrimer
+
+Welcome to the [AnoPrimer](https://github.com/sanjaynagi/AnoPrimer/) documentation!
+
+AnoPrimer is a python package for primer design in *An. gambiae* and *An. funestus*, whilst considering genetic variation in wild whole-genome sequenced specimens in malariagen_data.
+
+
+```{tableofcontents}
+```

docs/AnoPrimer-docs/notebooks/api.md

@@ -0,0 +1,45 @@
+# AnoPrimer API
+
+This notebook provides an overview of the API for the AnoPrimer python package, to design primers in *Anopheles* mosquitoes whilst considering genomic variation.
+
+## designPrimers()
+
+```{eval-rst}
+.. autofunction:: AnoPrimer::AnoPrimer.designPrimers
+```
+
+## plot_primer_snp_frequencies()
+
+```{eval-rst}
+.. autofunction:: AnoPrimer::AnoPrimer.plot_primer_snp_frequencies
+```
+
+## plot_primer_locs()
+
+```{eval-rst}
+.. autofunction:: AnoPrimer::AnoPrimer.plot_primer_locs
+```
+
+## gget_blat_genome()
+
+```{eval-rst}
+.. autofunction:: AnoPrimer::AnoPrimer.gget_blat_genome
+```
+
+## primer_params()
+
+```{eval-rst}
+.. autofunction:: AnoPrimer::AnoPrimer.primer_params
+```
+
+## primer3_to_pandas()
+
+```{eval-rst}
+.. autofunction:: AnoPrimer::AnoPrimer.primer3_to_pandas
+```
+
+## primer3_run_statistics()
+
+```{eval-rst}
+.. autofunction:: AnoPrimer::AnoPrimer.primer3_run_statistics
+```

docs/AgamPrimer-docs/notebooks/notebooks.ipynb → docs/AnoPrimer-docs/notebooks/notebooks.ipynb

@@ -8,16 +8,16 @@
    "source": [
     "# Notebooks\n",
     "\n",
-    "As well as a standalone python package, AgamPrimer is organised into two jupyter notebooks, intended to be run in google colab:\n",
+    "As well as a standalone python package, AnoPrimer is organised into two jupyter notebooks, intended to be run in google colab:\n",
     "\n",
     "<br>\n",
     "</br>\n",
     "\n",
     "<div align=\"center\">\n",
     "\n",
-    "[![Custom badge](https://img.shields.io/endpoint?color=white&logo=Google%20Colab&url=https%3A%2F%2Fraw.githubusercontent.com%2Fsanjaynagi%2FAgamPrimer%2Fmain%2Fgraphics%2Fbadge.json)](https://colab.research.google.com/github/sanjaynagi/AgamPrimer/blob/main/notebooks/AgamPrimer-long.ipynb)\n",
+    "[![Custom badge](https://img.shields.io/endpoint?color=white&logo=Google%20Colab&url=https%3A%2F%2Fraw.githubusercontent.com%2Fsanjaynagi%2FAnoPrimer%2Fmain%2Fgraphics%2Fbadge.json)](https://colab.research.google.com/github/sanjaynagi/AnoPrimer/blob/main/notebooks/AnoPrimer-long.ipynb)\n",
     "\n",
-    "[![Custom badge](https://img.shields.io/endpoint?color=red&logo=Google%20Colab&url=https%3A%2F%2Fraw.githubusercontent.com%2Fsanjaynagi%2FAgamPrimer%2Fmain%2Fgraphics%2Fbadge-short.json)](https://colab.research.google.com/github/sanjaynagi/AgamPrimer/blob/main/notebooks/AgamPrimer-short.ipynb)\n",
+    "[![Custom badge](https://img.shields.io/endpoint?color=red&logo=Google%20Colab&url=https%3A%2F%2Fraw.githubusercontent.com%2Fsanjaynagi%2FAnoPrimer%2Fmain%2Fgraphics%2Fbadge-short.json)](https://colab.research.google.com/github/sanjaynagi/AnoPrimer/blob/main/notebooks/AnoPrimer-short.ipynb)\n",
     "\n",
     "</div>\n"
    ]

docs/AgamPrimer-docs/notebooks/troubleshooting_contributing.ipynb → docs/AnoPrimer-docs/notebooks/troubleshooting_contributing.ipynb

@@ -8,16 +8,16 @@
    "source": [
     "# Troubleshooting\n",
     "\n",
-    "If you run into a problem or find a bug in the notebooks, please raise an issue to the [issue tracker](https://github.com/sanjaynagi/AgamPrimer/issues). \n",
+    "If you run into a problem or find a bug in the notebooks, please raise an issue to the [issue tracker](https://github.com/sanjaynagi/AnoPrimer/issues). \n",
     "\n",
     "If its not for a bug, but for general help and guidance, you may also [email](mailto:sanjay.c.nagi@gmail.com) me directly.\n",
     "\n",
     "\n",
     "# Contributing\n",
     "\n",
-    "We encourage contributions to AgamPrimer.\n",
+    "We encourage contributions to AnoPrimer.\n",
     "\n",
-    "If you have any feedback on how the repo may be improved, please do get in touch by emailing or raising an [issue on github](https://github.com/sanjaynagi/AgamPrimer/issues), or fork the github repository and create a pull request for any additional features you would like to implement."
+    "If you have any feedback on how the repo may be improved, please do get in touch by emailing or raising an [issue on github](https://github.com/sanjaynagi/AnoPrimer/issues), or fork the github repository and create a pull request for any additional features you would like to implement."
    ]
   }
  ],

docs/AgamPrimer-docs/requirements.txt → docs/AnoPrimer-docs/requirements.txt

@@ -1,4 +1,4 @@
 jupyter-book
 matplotlib
 numpy
-AgamPrimer
+AnoPrimer