RP3Net 0.0.1__tar.gz → 0.0.2__tar.gz

{rp3net-0.0.1 → rp3net-0.0.2}/.github/workflows/pypi-publish.yml

@@ -1,4 +1,4 @@
-name: Publish Python distribution to PyPI and TestPyPI
+name: Publish Python distribution to PyPI
 
 on: 
   push:

{rp3net-0.0.1 → rp3net-0.0.2}/.github/workflows/python-app.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: Build and test RP3Net without training dependencies
+name: CI
 
 on:
   push:

{rp3net-0.0.1 → rp3net-0.0.2}/.github/workflows/testpypi-publish.yml

@@ -1,4 +1,4 @@
-name: Publish Python distribution to PyPI and TestPyPI
+name: Publish Python distribution to TestPyPI
 
 on: 
   push:

rp3net-0.0.2/Dockerfile

@@ -0,0 +1,26 @@
+# docker build --platform linux/amd64 -t rp3net:test_1 .
+FROM pytorch/pytorch:2.5.1-cuda12.4-cudnn9-runtime
+
+RUN apt-get update && \
+    apt-get install -y git wget && \
+    mkdir -p /rp3/python && \
+    cd /rp3 && \
+    python -m venv --clear --system-site-packages python && \
+    /rp3/python/bin/pip install --upgrade pip && \
+    /rp3/python/bin/pip install RP3Net jupyter && \
+    /rp3/python/bin/jupyter server --generate-config && \
+    wget -nv -nc https://ftp.ebi.ac.uk/pub/software/RP3Net/v0.1/checkpoints/rp3net_v0.1_d.ckpt && \
+    wget -nv -nc https://raw.githubusercontent.com/RP3Net/RP3Net/refs/heads/main/rp3_colab.ipynb
+
+# /root/.jupyter/jupyter_server_config.py is generarated by `jupyter server --generate-config`
+RUN <<EOT cat >> /root/.jupyter/jupyter_server_config.py
+c.ServerApp.ip = '0.0.0.0'
+c.ServerApp.open_browser = False
+c.ServerApp.allow_root = True
+c.ExtensionApp.open_browser = False
+c.IdentityProvider.token = ''
+EOT
+
+ENV PATH="/rp3/python/bin:$PATH"
+WORKDIR /rp3
+EXPOSE 8888

{rp3net-0.0.1 → rp3net-0.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RP3Net
-Version: 0.0.1
+Version: 0.0.2
 Summary: RP3Net: Modelling of recombinant soluble protein production in E. coli
 Maintainer-email: Evgeny Tankhilevich <evgeny@ebi.ac.uk>
 License: MIT
@@ -14,7 +14,7 @@ Requires-Dist: torch==2.5.*
 Requires-Dist: pandas
 Requires-Dist: transformers==4.46.*
 Requires-Dist: ml_collections
-Requires-Dist: peft
+Requires-Dist: peft<0.18
 Requires-Dist: tqdm
 Provides-Extra: training
 Requires-Dist: lightning[pytorch-extra]==2.4.*; extra == "training"
@@ -23,8 +23,24 @@ Requires-Dist: wandb; extra == "training"
 Dynamic: license-file
 
 # RP3Net
+
+[![CI](https://github.com/RP3Net/RP3Net/actions/workflows/python-app.yml/badge.svg)](https://github.com/RP3Net/RP3Net/actions/workflows/python-app.yml)
+[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/RP3Net/RP3Net/blob/main/rp3_colab.ipynb)
+[![DOI:10.1101/2025.05.13.652824](http://img.shields.io/badge/DOI-10.1101/2021.01.08.425840-B31B1B.svg)](https://doi.org/10.1101/2025.05.13.652824)
+[![PyPI - Version](https://img.shields.io/pypi/v/RP3Net)](https://pypi.org/project/RP3Net/)
+
 RP3Net is an AI model for predicting the results of recombinant small-scale protein production in _E. coli_ from the construct sequence. See [the preprint](https://www.biorxiv.org/content/10.1101/2025.05.13.652824v1) and [supplements](https://ftp.ebi.ac.uk/pub/software/RP3Net/) for more details on how it works.
 
+# Try it out
+The simplest way to run the model inference is to open the [Colab notebook](https://colab.research.google.com/github/RP3Net/RP3Net/blob/main/rp3_colab.ipynb), paste the sequeces in FASTA format into the first cell and hit `Runtime -> Run All`. Use a runtime with a GPU to speed things up.
+
+## Docker
+Another way to try out the model without disclosing the sequences is via the [Docker image](https://hub.docker.com/r/rp3net/rp3net): `docker pull rp3net/rp3net`. The image contains the binary installation of the package, the checkpoint, a Jupyter server and the notebook. It supports CUDA. To run the docker contaier from the command line, using mounts to send the data in and out:
+```
+docker run -v /path/to/my/files:/mnt/rp3 rp3net/rp3net rp3 -p rp3net_v0.1_d.ckpt -f /mnt/rp3/sequences.fasta.gz -o /mnt/rp3/scores.csv.gz --log_file /dev/null
+```
+To interact with the container via the notebook, run `docker run -p 8888:8888 rp3net/rp3net jupyter lab`, open http://localhost:8888 in the browser and open `rp3_colab.ipynb`. There is no need to download the checkpoint and install the dependencies.
+
 # Checkpoints
 * https://ftp.ebi.ac.uk/pub/software/RP3Net/v0.1/checkpoints/
 

{rp3net-0.0.1 → rp3net-0.0.2}/README.md

@@ -1,6 +1,22 @@
 # RP3Net
+
+[![CI](https://github.com/RP3Net/RP3Net/actions/workflows/python-app.yml/badge.svg)](https://github.com/RP3Net/RP3Net/actions/workflows/python-app.yml)
+[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/RP3Net/RP3Net/blob/main/rp3_colab.ipynb)
+[![DOI:10.1101/2025.05.13.652824](http://img.shields.io/badge/DOI-10.1101/2021.01.08.425840-B31B1B.svg)](https://doi.org/10.1101/2025.05.13.652824)
+[![PyPI - Version](https://img.shields.io/pypi/v/RP3Net)](https://pypi.org/project/RP3Net/)
+
 RP3Net is an AI model for predicting the results of recombinant small-scale protein production in _E. coli_ from the construct sequence. See [the preprint](https://www.biorxiv.org/content/10.1101/2025.05.13.652824v1) and [supplements](https://ftp.ebi.ac.uk/pub/software/RP3Net/) for more details on how it works.
 
+# Try it out
+The simplest way to run the model inference is to open the [Colab notebook](https://colab.research.google.com/github/RP3Net/RP3Net/blob/main/rp3_colab.ipynb), paste the sequeces in FASTA format into the first cell and hit `Runtime -> Run All`. Use a runtime with a GPU to speed things up.
+
+## Docker
+Another way to try out the model without disclosing the sequences is via the [Docker image](https://hub.docker.com/r/rp3net/rp3net): `docker pull rp3net/rp3net`. The image contains the binary installation of the package, the checkpoint, a Jupyter server and the notebook. It supports CUDA. To run the docker contaier from the command line, using mounts to send the data in and out:
+```
+docker run -v /path/to/my/files:/mnt/rp3 rp3net/rp3net rp3 -p rp3net_v0.1_d.ckpt -f /mnt/rp3/sequences.fasta.gz -o /mnt/rp3/scores.csv.gz --log_file /dev/null
+```
+To interact with the container via the notebook, run `docker run -p 8888:8888 rp3net/rp3net jupyter lab`, open http://localhost:8888 in the browser and open `rp3_colab.ipynb`. There is no need to download the checkpoint and install the dependencies.
+
 # Checkpoints
 * https://ftp.ebi.ac.uk/pub/software/RP3Net/v0.1/checkpoints/
 

{rp3net-0.0.1 → rp3net-0.0.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "RP3Net"
-version = "0.0.1"
+version = "0.0.2"
 description = "RP3Net: Modelling of recombinant soluble protein production in E. coli"
 readme = "README.md"
 requires-python = ">=3.10,<4.0"
@@ -22,7 +22,7 @@ dependencies = [
     "pandas",
     "transformers==4.46.*",
     "ml_collections",
-    "peft",
+    "peft<0.18",
     "tqdm"
 ]
 

rp3net-0.0.2/rp3_colab.ipynb

@@ -0,0 +1,221 @@
+{
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": 9,
+      "id": "48f4e51a",
+      "metadata": {
+        "id": "48f4e51a"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Enter the construct sequences in FASTA format and hit `Runtime` -> `Run all`\n",
+        "batch_size = 4 # @param {\"type\":\"integer\"}\n",
+        "input_fasta = \"\"\"\n",
+        ">CONSTR_000001\n",
+        "MTVFFVTRLVKKHDKLSKQQIEDFAEKLMTILFETYRSHWHSDCPSKGQAFRCIRINNNQ\n",
+        "NKDPILERACVESNVDFSHLGLPKEMTIWVDPFEVCCRYGEKNHPFTVASFKGRWEEWEL\n",
+        "YQQISYAVSRASSDVSSGTSCDEESCGSHHHHHH\n",
+        ">CONSTR_000002\n",
+        "MDYTKPLEHPPVKRNEEAQVHDKLNSGMVSNMEGTAGGERPSVVNGDSGKSGGVGDPREP\n",
+        "LGCLQEGSGCHPTTESFEKSVREDASPLPHVCCCKQDALILQRGLHHEDGSQHIGLLHPG\n",
+        "DRGPDHEYVLVEEAECGSHHHHHH\n",
+        ">CONSTR_000003\n",
+        "MHHHHHHENLYFQGSLEVRGQLQSALLILGEPKEGGMPMNISIMPSSLQMKTPEGCTEIQ\n",
+        "LPAEVRLVPSSCRGLQFVVGDGLHLRLQTQAKLGTKLISMFNQSSQTQE\n",
+        ">CONSTR_000004\n",
+        "MECPEGQLPISSENDSTPTVSTSEVTSQQEPQILVDRGSETTYESSADIAGDEGTQIPAD\n",
+        "EDTQTDADSSAQAAAQAPENFQEGKDMSESQDEVPDEVENGSHHHHHH\n",
+        ">CONSTR_000005\n",
+        "MSTAPSEDIWKKFELVPSPPTSPPWGLGPGAGDPAPGIGPPEPWPGGCTGDEAESRGHSK\n",
+        "GWGRNYASIIRRDCMWSGFSARERLERAVSDRLAPGAPRGNPPKASAAPDCTPSLEAGNP\n",
+        "APAAPCPLGEPKTQACSGSESPSDSENEEIDVVTVEKRQSLGIRKPVTITVRADPLDPCM\n",
+        "KHFHGSHHHHHH\n",
+        ">CONSTR_000006\n",
+        "MEKARHETFAAEMRQNDKIMCILENRKKRDRKNLCRAINDFQQSFQKPETRREFDLSDPL\n",
+        "ALKKDLPARQSDNDVRNTISGMQGSHHHHHH\n",
+        ">CONSTR_000007\n",
+        "MLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILE\n",
+        "TLKRRGIGLDGPELEPDEGPEEPGEKFRRLAGEGGDPGSHHHHHH\n",
+        ">CONSTR_000008\n",
+        "MPTESASCSTARQTKQKRKSHSLSIRRTNSSEQERTGLPRDMLEGQDSKLPSSVRSTLLE\n",
+        "LFGQIEREFENLYIENLELRREIDTLNERLAAEGQAIDGAELSKGQLKTKASHSTSQLSQ\n",
+        "KLKTTYKASTSKIVSSFKTTTSRAACQLVKEYIGHRDGIWDVSVAKTQPVVLGTASADHT\n",
+        "ALLWSIETGKCLVKYAGHVGSVNSIKFHPSEQLALTASGDQTAHIWRYAVQLPTPQPVAD\n",
+        "TSISGEDEVECSDKDEPDLDGDVSSDCPTIRVPLTSLKSHQGVVIASDWLVGGKQAVTAS\n",
+        "WDRTANLYDVETSELVHSLTGHDQELTHCCTHPTQRLVVTSSRDTTFRLWDFRDPSIHSV\n",
+        "NVFQGHTDTVTSAVFTVGDNVVSGSDDRTVKVWDLKNMRSPIATIRTDSAINRINVCVGQ\n",
+        "KIIALPHDNRQVRLFDMSGVRLARLPRSSRQGHRRMVCCSAWSEDHPVCNLFTCGFDRQA\n",
+        "IGWNINIPALLQEKGSHHHHHH\n",
+        ">CONSTR_000009\n",
+        "MHHHHHHENLYFQGSPTESASCSTARQTKQKRKSHSLSIRRTNSSEQERTGLPRDMLEGQ\n",
+        "DSKLPSSVRSTLLELFGQIEREFENLYIENLELRREIDTLNERLAAEGQAIDGAELSKGQ\n",
+        "LKTKASHSTSQLSQKLKTTYKASTSKIVSSFKTTTSRAACQLVKEYIGHRDGIWDVSVAK\n",
+        "TQPVVLGTASADHTALLWSIETGKCLVKYAGHVGSVNSIKFHPSEQLALTASGDQTAHIW\n",
+        "RYAVQLPTPQPVADTSISGEDEVECSDKDEPDLDGDVSSDCPTIRVPLTSLKSHQGVVIA\n",
+        "SDWLVGGKQAVTASWDRTANLYDVETSELVHSLTGHDQELTHCCTHPTQRLVVTSSRDTT\n",
+        "FRLWDFRDPSIHSVNVFQGHTDTVTSAVFTVGDNVVSGSDDRTVKVWDLKNMRSPIATIR\n",
+        "TDSAINRINVCVGQKIIALPHDNRQVRLFDMSGVRLARLPRSSRQGHRRMVCCSAWSEDH\n",
+        "PVCNLFTCGFDRQAIGWNINIPALLQEK\n",
+        ">CONSTR_000010\n",
+        "MRDEIATTVFFVTRLVKKHDKLSKQQIEDFAEKLMTILFETYRSHWHSDCPSKGQAFRCI\n",
+        "RINNNQNKDPILERACVESNVDFSHLGLPKEMTIWVDPFEVCCRYGEKNHPFTVASFKGR\n",
+        "WEEWELYQQISYAVSRASSDVSSGTSCDEESCSKEPRVIPKVSNPKSIYQVENLKQPFQS\n",
+        "WLQIPRKKNVVDGRVGLLGNTYHGSQKHPKCYRPAMHRLDRILGSHHHHHH\n",
+        "\"\"\""
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "id": "b5e9d39a",
+      "metadata": {
+        "cellView": "form",
+        "collapsed": true,
+        "id": "b5e9d39a"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Install the dependencies and download the checkpoint\n",
+        "%%bash\n",
+        "\n",
+        "set -e\n",
+        "\n",
+        "pip install RP3Net 'torchvision==0.20.1'\n",
+        "wget -nv -nc https://ftp.ebi.ac.uk/pub/software/RP3Net/v0.1/checkpoints/rp3net_v0.1_d.ckpt"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": 5,
+      "id": "15ec2247",
+      "metadata": {
+        "cellView": "form",
+        "id": "15ec2247"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Imports\n",
+        "import re\n",
+        "import io\n",
+        "import pandas as pd\n",
+        "import RP3Net as rp3\n",
+        "from tqdm.notebook import tqdm\n",
+        "RE_FASTA_HEADER = re.compile(r'^>([\\w\\-.:#*]+)') # https://www.ncbi.nlm.nih.gov/genbank/fastaformat/"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": 6,
+      "id": "c5d31cfc",
+      "metadata": {
+        "cellView": "form",
+        "id": "c5d31cfc"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Helper functions\n",
+        "def iter_fasta(io):\n",
+        "    fasta_id, sequence = None, None\n",
+        "    for line in io:\n",
+        "        line = line.strip()\n",
+        "        if len(line) == 0:\n",
+        "            continue\n",
+        "        m = RE_FASTA_HEADER.match(line)\n",
+        "        if m:\n",
+        "            if fasta_id is not None:\n",
+        "                yield fasta_id, ''.join(sequence)\n",
+        "            sequence = []\n",
+        "            fasta_id = m.group(1)\n",
+        "        else:\n",
+        "            sequence.append(line)\n",
+        "    if fasta_id is not None:\n",
+        "        yield fasta_id, ''.join(sequence)\n",
+        "\n",
+        "def parse_fasta(s):\n",
+        "    return {id: seq for id, seq in iter_fasta(io.StringIO(s))}\n",
+        "\n",
+        "def batches():\n",
+        "    fasta_map = parse_fasta(input_fasta)\n",
+        "    fasta_keys = list(fasta_map.keys())\n",
+        "    r = tqdm(range(0, len(fasta_map), batch_size), desc='RP3Net Inference')\n",
+        "    for i in r:\n",
+        "        yield {k: fasta_map[k] for k in fasta_keys[i:i + batch_size]}"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": 7,
+      "id": "b9721c04",
+      "metadata": {
+        "id": "b9721c04"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Load the model\n",
+        "m = rp3.load_model(rp3.RP3_DEFAULT_CONFIG, 'rp3net_v0.1_d.ckpt')\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "id": "z1-PoDkqoVSc",
+      "metadata": {
+        "id": "z1-PoDkqoVSc",
+        "outputId": "5a788b91-2bdf-419f-c524-2c70cd56c2af"
+      },
+      "outputs": [],
+      "source": [
+        "#@title Run the prediction on GPU\n",
+        "m = m.to(device='cuda')\n",
+        "scores_map = dict()\n",
+        "for b in batches():\n",
+        "    scores_map |= m.predict(b, device='cuda')\n"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": 11,
+      "id": "BvfWdEhXpiGJ",
+      "metadata": {
+        "colab": {
+          "base_uri": "https://localhost:8080/"
+        },
+        "id": "BvfWdEhXpiGJ",
+        "outputId": "f062f810-c709-4b00-c566-1b5b232f2585"
+      },
+      "outputs": [
+        {
+          "name": "stdout",
+          "output_type": "stream",
+          "text": [
+            "              id     score\n",
+            "0  CONSTR_000001  0.691543\n",
+            "1  CONSTR_000002  0.971137\n",
+            "2  CONSTR_000003  0.931065\n",
+            "3  CONSTR_000004  0.972745\n",
+            "4  CONSTR_000005  0.928140\n",
+            "5  CONSTR_000006  0.977404\n",
+            "6  CONSTR_000007  0.744749\n",
+            "7  CONSTR_000008  0.009805\n",
+            "8  CONSTR_000009  0.009679\n",
+            "9  CONSTR_000010  0.433345\n"
+          ]
+        }
+      ],
+      "source": [
+        "#@title Print and save the results\n",
+        "df = pd.DataFrame([[id, score] for (id, score) in scores_map.items()], columns=['id', 'score'])\n",
+        "print(df)\n",
+        "df.to_csv(\"rp3_scores.csv\", index=False)"
+      ]
+    }
+  ],
+  "metadata": {
+    "language_info": {
+      "name": "python"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 5
+}

{rp3net-0.0.1 → rp3net-0.0.2}/src/RP3Net.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RP3Net
-Version: 0.0.1
+Version: 0.0.2
 Summary: RP3Net: Modelling of recombinant soluble protein production in E. coli
 Maintainer-email: Evgeny Tankhilevich <evgeny@ebi.ac.uk>
 License: MIT
@@ -14,7 +14,7 @@ Requires-Dist: torch==2.5.*
 Requires-Dist: pandas
 Requires-Dist: transformers==4.46.*
 Requires-Dist: ml_collections
-Requires-Dist: peft
+Requires-Dist: peft<0.18
 Requires-Dist: tqdm
 Provides-Extra: training
 Requires-Dist: lightning[pytorch-extra]==2.4.*; extra == "training"
@@ -23,8 +23,24 @@ Requires-Dist: wandb; extra == "training"
 Dynamic: license-file
 
 # RP3Net
+
+[![CI](https://github.com/RP3Net/RP3Net/actions/workflows/python-app.yml/badge.svg)](https://github.com/RP3Net/RP3Net/actions/workflows/python-app.yml)
+[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/RP3Net/RP3Net/blob/main/rp3_colab.ipynb)
+[![DOI:10.1101/2025.05.13.652824](http://img.shields.io/badge/DOI-10.1101/2021.01.08.425840-B31B1B.svg)](https://doi.org/10.1101/2025.05.13.652824)
+[![PyPI - Version](https://img.shields.io/pypi/v/RP3Net)](https://pypi.org/project/RP3Net/)
+
 RP3Net is an AI model for predicting the results of recombinant small-scale protein production in _E. coli_ from the construct sequence. See [the preprint](https://www.biorxiv.org/content/10.1101/2025.05.13.652824v1) and [supplements](https://ftp.ebi.ac.uk/pub/software/RP3Net/) for more details on how it works.
 
+# Try it out
+The simplest way to run the model inference is to open the [Colab notebook](https://colab.research.google.com/github/RP3Net/RP3Net/blob/main/rp3_colab.ipynb), paste the sequeces in FASTA format into the first cell and hit `Runtime -> Run All`. Use a runtime with a GPU to speed things up.
+
+## Docker
+Another way to try out the model without disclosing the sequences is via the [Docker image](https://hub.docker.com/r/rp3net/rp3net): `docker pull rp3net/rp3net`. The image contains the binary installation of the package, the checkpoint, a Jupyter server and the notebook. It supports CUDA. To run the docker contaier from the command line, using mounts to send the data in and out:
+```
+docker run -v /path/to/my/files:/mnt/rp3 rp3net/rp3net rp3 -p rp3net_v0.1_d.ckpt -f /mnt/rp3/sequences.fasta.gz -o /mnt/rp3/scores.csv.gz --log_file /dev/null
+```
+To interact with the container via the notebook, run `docker run -p 8888:8888 rp3net/rp3net jupyter lab`, open http://localhost:8888 in the browser and open `rp3_colab.ipynb`. There is no need to download the checkpoint and install the dependencies.
+
 # Checkpoints
 * https://ftp.ebi.ac.uk/pub/software/RP3Net/v0.1/checkpoints/
 

{rp3net-0.0.1 → rp3net-0.0.2}/src/RP3Net.egg-info/SOURCES.txt

@@ -1,7 +1,9 @@
 .gitignore
+Dockerfile
 LICENSE
 README.md
 pyproject.toml
+rp3_colab.ipynb
 .github/workflows/pypi-publish.yml
 .github/workflows/python-app-training.yml
 .github/workflows/python-app.yml

{rp3net-0.0.1 → rp3net-0.0.2}/src/RP3Net.egg-info/requires.txt

@@ -2,7 +2,7 @@ torch==2.5.*
 pandas
 transformers==4.46.*
 ml_collections
-peft
+peft<0.18
 tqdm
 
 [training]