Merge pull request #101 from hgb-bin-proteomics/upgrade-dependencies

Upgrade dependencies and Dockerfile

Author: michabirklbauer

Dockerfile

@@ -1,6 +1,6 @@
 # Dockerfile for Internal Ion Explorer
 # author: Micha Birklbauer
-# version: 1.2.2
+# version: 1.3.0
 
 FROM python:3.12
 
@@ -10,10 +10,11 @@ RUN mkdir internal_ions
 COPY ./ internal_ions/
 WORKDIR internal_ions
 
-RUN python3 -m venv venv && \
-    . venv/bin/activate && \
-    pip install --upgrade pip && \
-    pip install --upgrade setuptools && \
-    pip install --no-cache-dir -r env.txt
+RUN pip install --upgrade pip
+RUN pip install --upgrade setuptools
+RUN pip install --no-cache-dir uv
 
-CMD  ["sh", "-c", ". venv/bin/activate && streamlit run streamlit_app.py"]
+RUN uv sync
+RUN uv cache clean
+
+CMD  ["sh", "-c", "uv run -- streamlit run streamlit_app.py"]

internal_ions/tab1.py

@@ -1,4 +1,5 @@
 import json
+import numpy as np
 
 import streamlit as st
 import logging
@@ -96,13 +97,13 @@ def main(argv=None) -> None:
         if st.session_state["sidebar_disabled"]:
             enable_sidebar = st.button("Re-enable upload and parameter selection!",
                                        type="secondary",
-                                       use_container_width=True)
+                                       width="stretch")
             if enable_sidebar:
                 st.session_state["sidebar_disabled"] = False
                 st.rerun()
         run_analysis = st.button("Load files and run Fragannot!",
                                  type="primary",
-                                 use_container_width=True)
+                                 width="stretch")
 
     if run_analysis:
         st.session_state["sidebar_disabled"] = True
@@ -136,7 +137,7 @@ def main(argv=None) -> None:
 
                         converter = JSONConverter()
                         st.session_state["result"] = result
-                        st.session_state["dataframes"] = converter.to_dataframes(data=result)
+                        st.session_state["dataframes"] = [df.replace(r'^\s*$', np.nan, regex=True) for df in converter.to_dataframes(data=result)]
                         st.session_state["dataframes_source"] = {"spectrum_file": spectrum_file.name,
                                                                  "identifications_file": st.session_state.identifications_file.name,
                                                                  "fragment_centric_csv": None,
@@ -160,9 +161,9 @@ def main(argv=None) -> None:
     if "dataframes" in st.session_state:
         st.subheader("Results Preview", divider=DIV_COLOR)
         st.markdown("Fragment-centric")
-        st.dataframe(st.session_state["dataframes"][0].head(10), use_container_width=True)
+        st.dataframe(st.session_state["dataframes"][0].head(10), width="stretch")
         st.markdown("Spectrum-centric")
-        st.dataframe(st.session_state["dataframes"][1].head(10), use_container_width=True)
+        st.dataframe(st.session_state["dataframes"][1].head(10), width="stretch")
 
         st.subheader("Download Results", divider=DIV_COLOR)
 
@@ -175,15 +176,15 @@ def main(argv=None) -> None:
                                mime="text/csv",
                                help="Download fragment-centric Fragannot results in .csv format.",
                                type="primary",
-                               use_container_width=True)
+                               width="stretch")
         with dl_center:
             st.download_button(label="Download Spectrum-centric data!",
                                data=dataframe_to_csv_stream(st.session_state["dataframes"][1]),
                                file_name="spectrum_centric.csv",
                                mime="text/csv",
                                help="Download spectrum-centric Fragannot results in .csv format.",
                                type="primary",
-                               use_container_width=True)
+                               width="stretch")
 
         if "result" in st.session_state:
             with dl_r1:
@@ -193,4 +194,4 @@ def main(argv=None) -> None:
                                    mime="text/json",
                                    help="Download raw Fragannot results in .json file format.",
                                    type="primary",
-                                   use_container_width=True)
+                                   width="stretch")

internal_ions/tab2.py

@@ -88,9 +88,9 @@ def main(argv=None) -> None:
                 st.session_state["spec_center_filtered"], st.session_state["frag_center_filtered"] = filter_dataframe(tmp_spec, tmp_frag, 'spectrum')
 
             st.markdown("Data of the fragment-centric dataframe:")
-            st.dataframe(st.session_state["frag_center_filtered"], height=400, use_container_width=True)
+            st.dataframe(st.session_state["frag_center_filtered"], height=400, width="stretch")
             st.markdown("Data of the spectrum-centric dataframe:")
-            st.dataframe(st.session_state["spec_center_filtered"], height=400, use_container_width=True)
+            st.dataframe(st.session_state["spec_center_filtered"], height=400, width="stretch")
 
     ############################################################################
 
@@ -101,47 +101,47 @@ def main(argv=None) -> None:
 
             with frag_center_plot_col1_1:
                 st.markdown("**Distribution of Ion Types**")
-                st.plotly_chart(common_type_hist(st.session_state["frag_center_filtered"]), use_container_width=True)
+                st.plotly_chart(common_type_hist(st.session_state["frag_center_filtered"]), width="stretch")
                 st.markdown("**Figure 1:** Histogram illustrating the frequency distribution of ion types present in the dataset.")
 
             with frag_center_plot_col1_2:
                 st.markdown("**Ion Type Proportions**")
-                st.plotly_chart(common_type_pie(st.session_state["frag_center_filtered"]), use_container_width=True)
+                st.plotly_chart(common_type_pie(st.session_state["frag_center_filtered"]), width="stretch")
                 st.markdown("**Figure 2:** Pie chart displaying the proportional composition of ion types within the dataset.")
 
             st.markdown("**Distribution of m/z Values Across Ion Types**")
-            st.plotly_chart(mz_dist_ion_type(st.session_state["frag_center_filtered"]), use_container_width=True)
+            st.plotly_chart(mz_dist_ion_type(st.session_state["frag_center_filtered"]), width="stretch")
             st.markdown("**Figure 3:** Histogram depicting the distribution of mass-to-charge ratio (m/z) values across different ion types.")
 
             frag_center_plot_col3_1, frag_center_plot_col3_2 = st.columns(2)
 
             with frag_center_plot_col3_1:
                 st.markdown("**Distribution of the Log Intensity**")
-                st.plotly_chart(rel_ion_intens_perc(st.session_state["frag_center_filtered"]), use_container_width=True)
+                st.plotly_chart(rel_ion_intens_perc(st.session_state["frag_center_filtered"]), width="stretch")
                 st.markdown("**Figure 4:** Distribution of log-transformed intensity values.")
 
             with frag_center_plot_col3_2:
                 st.markdown("**Relative Log Intensities**")
-                st.plotly_chart(rel_ion_intens_ridge(st.session_state["frag_center_filtered"]), use_container_width=True)
+                st.plotly_chart(rel_ion_intens_ridge(st.session_state["frag_center_filtered"]), width="stretch")
                 st.markdown("**Figure 5:** Distribution of log-transformed intensities relative to their respective scales.")
 
             frag_center_plot_col4_1, frag_center_plot_col4_2 = st.columns(2)
 
             with frag_center_plot_col4_1:
                 st.markdown("**Proportional Distribution of m/z Values**")
-                st.plotly_chart(proportional_distribution_of_mz_values(st.session_state["frag_center_filtered"]), use_container_width=True)
+                st.plotly_chart(proportional_distribution_of_mz_values(st.session_state["frag_center_filtered"]), width="stretch")
                 st.markdown("**Figure 6:** Proportional Distribution of m/z Values (Bin Size = 100).")
 
             with frag_center_plot_col4_2:
                 st.markdown("**First residue of internal and terminal ions**")
-                st.plotly_chart(first_residue_of_internal_and_terminal_ions(st.session_state["frag_center_filtered"]), use_container_width=True)
+                st.plotly_chart(first_residue_of_internal_and_terminal_ions(st.session_state["frag_center_filtered"]), width="stretch")
                 st.markdown("**Figure 7:** First residue of internal and terminal ions.")
 
             frag_center_plot_col5_1, frag_center_plot_col5_2 = st.columns(2)
 
             with frag_center_plot_col5_1:
                 st.markdown("**Last residue of internal and terminal ions**")
-                st.plotly_chart(last_residue_of_internal_and_terminal_ions(st.session_state["frag_center_filtered"]), use_container_width=True)
+                st.plotly_chart(last_residue_of_internal_and_terminal_ions(st.session_state["frag_center_filtered"]), width="stretch")
                 st.markdown("**Figure 8:** Last residue of internal and terminal ions.")
 
     ############################################################################
@@ -152,36 +152,36 @@ def main(argv=None) -> None:
 
             with spec_center_plot_col1_1:
                 st.markdown("**Ion Type Distribution Per Spectra**")
-                st.plotly_chart(per_spec_ion_type(st.session_state["spec_center_filtered"]), use_container_width=True)
+                st.plotly_chart(per_spec_ion_type(st.session_state["spec_center_filtered"]), width="stretch")
                 st.markdown("**Figure 9:** Distribution of ion types within each spectrum, providing insights into the diversity and abundance of ions detected across the dataset.")
 
             with spec_center_plot_col1_2:
                 st.markdown("**Log Intensities:**")
-                st.plotly_chart(per_spec_ion_intens(st.session_state["spec_center_filtered"]), use_container_width=True)
+                st.plotly_chart(per_spec_ion_intens(st.session_state["spec_center_filtered"]), width="stretch")
                 st.markdown("**Figure 10:** Distribution of log-transformed intensities.")
 
             spec_center_plot_col2_1, spec_center_plot_col2_2 = st.columns(2)
 
             with spec_center_plot_col2_1:
                 st.markdown("**Plot of the length of the top 1 internal ion**")
-                st.plotly_chart(density_plot_of_the_length_of_the_top_1_internal_ion(st.session_state["spec_center_filtered"]), use_container_width=True)
+                st.plotly_chart(density_plot_of_the_length_of_the_top_1_internal_ion(st.session_state["spec_center_filtered"]), width="stretch")
                 st.markdown("**Figure 11:** Plot of the length of the top 1 internal ion.")
 
             with spec_center_plot_col2_2:
                 st.markdown("**Plot of the length of the top 2 internal ion:**")
-                st.plotly_chart(density_plot_of_the_length_of_the_top_2_internal_ion(st.session_state["spec_center_filtered"]), use_container_width=True)
+                st.plotly_chart(density_plot_of_the_length_of_the_top_2_internal_ion(st.session_state["spec_center_filtered"]), width="stretch")
                 st.markdown("**Figure 12:** Plot of the length of the top 2 internal ion.")
 
             spec_center_plot_col3_1, spec_center_plot_col3_2 = st.columns(2)
 
             with spec_center_plot_col3_1:
                 st.markdown("**Plot of the length of the top 3 internal ion**")
-                st.plotly_chart(density_plot_of_the_length_of_the_top_3_internal_ion(st.session_state["spec_center_filtered"]), use_container_width=True)
+                st.plotly_chart(density_plot_of_the_length_of_the_top_3_internal_ion(st.session_state["spec_center_filtered"]), width="stretch")
                 st.markdown("**Figure 13:** Plot of the length of the top 3 internal ion.")
 
             with spec_center_plot_col3_2:
                 st.markdown("**Plot of the length of the top internal ions:**")
-                st.plotly_chart(density_plot_of_the_length_of_the_top_internal_ions(st.session_state["spec_center_filtered"]), use_container_width=True)
+                st.plotly_chart(density_plot_of_the_length_of_the_top_internal_ions(st.session_state["spec_center_filtered"]), width="stretch")
                 st.markdown("**Figure 14:** Plot of the length of the top internal ions.")
 
             st.markdown("**Logo view of internal fragments:**")

internal_ions/tab3.py

@@ -76,7 +76,7 @@ def main(argv=None) -> None:
 
         # plot chromatogram
         spectra_chromatogram = st.plotly_chart(plot_spectra_chromatogram(spectra["spectra"]),
-                                               use_container_width=True,
+                                               width="stretch",
                                                theme="streamlit",
                                                key="chromatogram",
                                                on_select="rerun",
@@ -201,7 +201,7 @@ def main(argv=None) -> None:
         with center_button:
             run_filter = st.button("Filter spectra and create consensus spectrum",
                                    type="primary",
-                                   use_container_width=True)
+                                   width="stretch")
 
         if run_filter:
             selected_scans_list = [i for i in range(int(first_scan), int(last_scan) + 1)]
@@ -267,7 +267,7 @@ def main(argv=None) -> None:
                                                 st.session_state["consensus_spectrum"]["mz_mean"],
                                                 st.session_state["consensus_spectrum"]["cov_spectra"]
                                                 )
-        st.plotly_chart(spectrum_plot, use_container_width=True)
+        st.plotly_chart(spectrum_plot, width="stretch")
         st.markdown("**Figure 1:** Displaying consensus spetrum.")
 
     if "consensus_spectrum" in st.session_state:
@@ -337,7 +337,7 @@ def main(argv=None) -> None:
         if "generated_fraggraph" not in st.session_state:
             fg_run_l, fg_run_center, fg_run_r = st.columns(3)
             with fg_run_center:
-                run_fraggraph = st.button("Run Fraggraph!", type="primary", use_container_width=True)
+                run_fraggraph = st.button("Run Fraggraph!", type="primary", width="stretch")
 
         if "generated_fraggraph" in st.session_state or run_fraggraph:
             st.session_state["generated_fraggraph"] = True

internal_ions/tab4.py

@@ -21,4 +21,4 @@ def main(argv=None) -> None:
         ext_docs = st.link_button("Read full documentation!",
                                   url = "https://internal-ions.vercel.app/",
                                   type = "primary",
-                                  use_container_width = True)
+                                  width = "stretch")