Merge pull request #52 from compomics/update-streamlit

Fix Streamlit web server
compomics · May 16, 2023 · 34bf725 · 34bf725
2 parents c0b9c98 + fb926ab
commit 34bf725
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Showing 7 changed files with 55 additions and 77 deletions.
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -2,8 +2,8 @@ name: Publish to PyPI and GitHub release
 
 on:
   push:
-  #   tags:
-  #   - 'v*'
+    tags:
+    - 'v*'
 
 jobs:
   python-package:
@@ -83,6 +83,7 @@ jobs:
 
   build-streamlit-image:
     runs-on: ubuntu-latest
+    needs: python-package
     steps:
     - uses: actions/checkout@v2
     - id: latest_release

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -11,25 +11,25 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.9', '3.10']
+        python-version: ["3.9", "3.10"]
         os: [ubuntu-latest, windows-latest, macos-latest]
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        pip install --editable .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          pip install --editable .
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest
diff --git a/streamlit/Dockerfile b/streamlit/Dockerfile
@@ -1,19 +1,7 @@
-FROM continuumio/miniconda3:4.9.2 AS build
-COPY environment.yml /
-RUN conda env create -f environment.yml && \
-    conda install -c conda-forge conda-pack && \
-    conda-pack -n deeplc-streamlit -o /tmp/env.tar && \
-    mkdir /venv && cd /venv && tar xf /tmp/env.tar && \
-    rm /tmp/env.tar && \
-    /venv/bin/conda-unpack
-
-FROM debian:buster-slim AS runtime
-WORKDIR /deeplc
-COPY --from=build /venv /venv
-ENV VIRTUAL_ENV=/venv
-ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+FROM python:3.10-slim-buster
 COPY . /deeplc
-RUN pip install "deeplc>=0.1.29"
+WORKDIR /deeplc
+RUN pip install --upgrade pip && pip install -r requirements.txt
 ENV DEEPLC_LIBRARY_PATH="/tmp/deeplc_library.txt"
 EXPOSE 8501
 CMD ["streamlit", "run", "deeplc_streamlit.py"]
diff --git a/streamlit/deeplc_streamlit.py b/streamlit/deeplc_streamlit.py
@@ -8,10 +8,10 @@
 
 import pandas as pd
 import plotly.express as px
-from deeplc import DeepLC
+from streamlit_utils import hide_streamlit_menu, save_dataframe
 
 import streamlit as st
-from streamlit_utils import hide_streamlit_menu, save_dataframe
+from deeplc import DeepLC
 
 logger = logging.getLogger(__name__)
 
@@ -101,7 +101,10 @@ def _main_page(self):
                     help=self.texts.Help.dict_cal_divider,
                 )
                 self.user_input["split_cal"] = st.number_input(
-                    "Split calibration", step=1, value=25, help=self.texts.Help.split_cal
+                    "Split calibration",
+                    step=1,
+                    value=25,
+                    help=self.texts.Help.split_cal,
                 )
 
             st.subheader("Prediction speed boost")
@@ -145,7 +148,10 @@ def _run_deeplc(self):
 
         logger.info(
             "Run requested // %s // peptides %i / use_library %r / calibrate %r",
-            datetime.now(), len(config["input_df"]), use_lib, calibrate
+            datetime.now(),
+            len(config["input_df"]),
+            use_lib,
+            calibrate,
         )
 
         # Run DeepLC
@@ -161,9 +167,7 @@ def _run_deeplc(self):
                 reload_library=True if use_lib else False,
             )
             if calibrate:
-                config["input_df_calibration"]["modifications"].fillna(
-                    "", inplace=True
-                )
+                config["input_df_calibration"]["modifications"].fillna("", inplace=True)
                 dlc.calibrate_preds(seq_df=config["input_df_calibration"])
             config["input_df"]["modifications"].fillna("", inplace=True)
             preds = dlc.make_preds(seq_df=config["input_df"], calibrate=calibrate)
@@ -191,7 +195,7 @@ def _run_deeplc(self):
                 label="Download",
                 data=save_dataframe(result_df),
                 file_name="deeplc_predictions.csv",
-                mime="text/csv"
+                mime="text/csv",
             )
 
     def _set_library_path(self):
@@ -241,7 +245,7 @@ def _parse_user_config(self, user_input):
             try:
                 config["input_df"] = pd.read_csv(user_input["input_csv"])
             except (ValueError, pd.errors.ParserError) as e:
-                raise InvalidPeptideCSV(e)
+                raise InvalidPeptideCSV(e) from e
         else:
             raise MissingPeptideCSV
 
@@ -260,7 +264,7 @@ def _parse_user_config(self, user_input):
                         user_input["input_csv_calibration"]
                     )
                 except (ValueError, pd.errors.ParserError) as e:
-                    raise InvalidPeptideCSV(e)
+                    raise InvalidPeptideCSV(e) from e
 
         return config
 
@@ -306,7 +310,7 @@ class Sidebar:
         badges = """
             [![GitHub release](https://img.shields.io/github/release-pre/compomics/deeplc.svg?style=flat-square)](https://github.com/compomics/deeplc/releases)
             [![GitHub](https://img.shields.io/github/license/compomics/deeplc.svg?style=flat-square)](https://www.apache.org/licenses/LICENSE-2.0)
-            [![Twitter](https://flat.badgen.net/twitter/follow/compomics?icon=twitter)](https://twitter.com/compomics)
+            [![Twitter](https://img.shields.io/twitter/follow/compomics?style=flat-square)](https://twitter.com/compomics)
             """
 
         about = f"""
@@ -323,18 +327,19 @@ class Sidebar:
             If you use DeepLC for your research, please use the following citation:
             >**DeepLC can predict retention times for peptides that carry as-yet unseen
             modifications**<br>
-            >Robbin Bouwmeester, Ralf Gabriels, Niels Hulstaert, Lennart Martens, Sven
-            Degroeve<br>
-            >_bioRxiv (2020)_<br>
-            >[doi:10.1101/2020.03.28.013003](https://doi.org/10.1101/2020.03.28.013003)
+            >Robbin Bouwmeester, Ralf Gabriels, Niels Hulstaert, Lennart Martens, Sven Degroeve<br>
+            >_Nature Methods 18, 1363–1369 (2021)_<br>
+            >[doi:10.1038/s41592-021-01301-5](https://doi.org/10.1038/s41592-021-01301-5)
 
             ---
 
-            Currently using the following package versions:
+            Currently using the following package versions: <br />
+            [![DeepLC](https://img.shields.io/badge/deeplc-{version('deeplc')}-blue?style=flat-square&logoColor=white&logo=pypi)](https://github.com/compomics/deeplc)
+            [![Tensorflow](https://img.shields.io/badge/tensorflow-{version('tensorflow')}-blue?style=flat-square&logoColor=white&logo=pypi)](https://github.com/tensorflow/tensorflow)
+            [![Streamlit](https://img.shields.io/badge/streamlit-{version('streamlit')}-blue?style=flat-square&logoColor=white&logo=pypi)](https://github.com/streamlit/streamlit)
 
-            [![DeepLC](https://flat.badgen.net/badge/deeplc/{version('deeplc')}/grey?icon=pypi)](https://github.com/compomics/deeplc)
-            [![Tensorflow](https://flat.badgen.net/badge/tensorflow/{version('tensorflow')}/grey?icon=pypi)](https://github.com/tensorflow/tensorflow)
-            [![Streamlit](https://flat.badgen.net/badge/streamlit/{version('streamlit')}/grey?icon=pypi)](https://github.com/streamlit/streamlit)
+            Latest DeepLC version:<br />
+            ![PyPI](https://img.shields.io/pypi/v/deeplc?style=flat-square&logoColor=white&logo=pypi)
             """
 
     class Help:

diff --git a/streamlit/environment.yml b/streamlit/environment.yml
diff --git a/streamlit/requirements.txt b/streamlit/requirements.txt
@@ -0,0 +1,5 @@
+plotly
+pandas
+statsmodels
+streamlit>=0.88
+deeplc
diff --git a/streamlit/streamlit_utils.py b/streamlit/streamlit_utils.py
@@ -1,16 +1,6 @@
 """Streamlit utils."""
 
-import base64
-import io
 import logging
-import os
-import re
-import tempfile
-import uuid
-import zipfile
-from typing import BinaryIO
-
-from typing_extensions import get_origin
 
 import streamlit as st