resolved conflitcs

.github/workflows/ci.yml

@@ -12,16 +12,20 @@ jobs:
         python-version: ["3.11"]
     steps:
     - uses: actions/checkout@v4
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+    - uses: conda-incubator/setup-miniconda@v3
       with:
+        activate-environment: openms
         python-version: ${{ matrix.python-version }}
+        channels: defaults,bioconda,conda-forge
+
+    - name: Install OpenMS
+      run: |
+        conda install openms -y
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt # test with requirements file so can easily bump with dependabot
         pip install pytest
     - name: Test
       run: |
-        python -m pytest test_gui.py 
+        python -m pytest test_gui.py

app.py

@@ -1,11 +1,16 @@
 import streamlit as st
 from pathlib import Path
+import json
 # For some reason the windows version only works if this is imported here
 import pyopenms
 
+if "settings" not in st.session_state:
+        with open("settings.json", "r") as f:
+            st.session_state.settings = json.load(f)
+
 if __name__ == '__main__':
     pages = {
-        "OpenMS Web App" : [
+        str(st.session_state.settings["app-name"]) : [
             st.Page(Path("content", "quickstart.py"), title="Quickstart", icon="👋"),
             st.Page(Path("content", "documentation.py"), title="Documentation", icon="📖"),
         ],

environment.yml

@@ -1,17 +1,17 @@
 ###### TODO: how use exact version specifiers for all packages ######
 name: streamlit-env
 channels:
-- conda-forge
+   - conda-forge
 dependencies:
-- python==3.11
-- plotly==5.22.0
-- pip==24.0
-- numpy==1.26.4 # pandas and numpy are dependencies of pyopenms, however, pyopenms needs numpy<=1.26.4
-- mono==6.12.0.90
-- pip:
-  # dependencies only available through pip
-  # streamlit dependencies
-  - streamlit>=1.38.0
-  - captcha==0.5.0
-  - pyopenms_viz>=0.1.2
-  - streamlit-js-eval
+   - python==3.11
+   - plotly==5.22.0
+   - pip==24.0
+   - numpy==1.26.4 # pandas and numpy are dependencies of pyopenms, however, pyopenms needs numpy<=1.26.4
+   - mono==6.12.0.90
+   - pip:
+        # dependencies only available through pip
+        # streamlit dependencies
+        - streamlit>=1.38.0
+        - captcha==0.5.0
+        - pyopenms_viz==1.0.0
+        - streamlit-js-eval

requirements.txt

@@ -6,7 +6,7 @@ pyopenms==3.2.0
 numpy==1.26.4 # pandas and numpy are dependencies of pyopenms, however, pyopenms needs numpy<=1.26.4
 plotly==5.22.0
 captcha==0.5.0
-pyopenms_viz>=0.1.2
+pyopenms_viz==1.0.0
 streamlit-js-eval
 redis==5.2.1
-rq==2.1.0
+rq==2.1.0

settings.json

@@ -1,6 +1,7 @@
 {
     "app-name": "OpenMS WebApp Template",
     "github-user": "OpenMS",
+    "version": "1.0.2",
     "repository-name": "streamlit-template",
     "analytics": {
         "google-analytics": {
@@ -13,5 +14,6 @@
         }
     },
     "online_deployment": false,
+    "enable_workspaces": true,
     "test": true
 }

src/common/common.py

@@ -41,6 +41,11 @@ def load_params(default: bool = False) -> dict[str, Any]:
     Returns:
         dict[str, Any]: A dictionary containing the parameters.
     """
+
+    # Check if workspace is enabled. If not, load default parameters.
+    if not st.session_state.settings["enable_workspaces"]:
+        default = True
+
     # Construct the path to the parameter file
     path = Path(st.session_state.workspace, "params.json")
 
@@ -75,6 +80,11 @@ def save_params(params: dict[str, Any]) -> None:
     Returns:
         dict[str, Any]: Updated parameters.
     """
+
+    # Check if the workspace is enabled and if a 'params.json' file exists in the workspace directory
+    if not st.session_state.settings["enable_workspaces"]:
+        return
+
     # Update the parameter dictionary with any modified parameters from the current session
     for key, value in st.session_state.items():
         if key in params.keys():
@@ -199,21 +209,28 @@ def page_setup(page: str = "") -> dict[str, Any]:
             os.chdir("../streamlit-template")
         # Define the directory where all workspaces will be stored
         workspaces_dir = Path("..", "workspaces-" + st.session_state.settings["repository-name"])
-        if "workspace" in st.query_params:
-            st.session_state.workspace = Path(workspaces_dir, st.query_params.workspace)
-        elif st.session_state.location == "online":
-            workspace_id = str(uuid.uuid1())
-            st.session_state.workspace = Path(workspaces_dir, workspace_id)
-            st.query_params.workspace = workspace_id
+        # Check if workspace logic is enabled
+        if st.session_state.settings["enable_workspaces"]:
+            if "workspace" in st.query_params:
+                    st.session_state.workspace = Path(workspaces_dir, st.query_params.workspace)
+            elif st.session_state.location == "online":
+                    workspace_id = str(uuid.uuid1())
+                    st.session_state.workspace = Path(workspaces_dir, workspace_id)
+                    st.query_params.workspace = workspace_id
+            else:
+                st.session_state.workspace = Path(workspaces_dir, "default")
+                st.query_params.workspace = "default"
+
         else:
+            # Use default workspace when workspace feature is disabled
             st.session_state.workspace = Path(workspaces_dir, "default")
-            st.query_params.workspace = "default"
 
         if st.session_state.location != "online":
             # not any captcha so, controllo should be true
             st.session_state["controllo"] = True
 
-    if "workspace" not in st.query_params:
+    # If no workspace is specified and workspace feature is enabled, set default workspace and query param
+    if "workspace" not in st.query_params and st.session_state.settings["enable_workspaces"]:
         st.query_params.workspace = st.session_state.workspace.name
 
     # Make sure the necessary directories exist
@@ -259,51 +276,53 @@ def render_sidebar(page: str = "") -> None:
     params = load_params()
     with st.sidebar:
         # The main page has workspace switcher
-        with st.expander("🖥️ **Workspaces**"):
-            # Define workspaces directory outside of repository
-            workspaces_dir = Path("..", "workspaces-" + st.session_state.settings["repository-name"])
-            # Online: show current workspace name in info text and option to change to other existing workspace
-            if st.session_state.location == "local":
-                # Define callback function to change workspace
-                def change_workspace():
-                    for key in params.keys():
-                        if key in st.session_state.keys():
-                            del st.session_state[key]
-                    st.session_state.workspace = Path(
-                        workspaces_dir, st.session_state["chosen-workspace"]
+        # Display workspace switcher if workspace is enabled in local mode
+        if st.session_state.settings["enable_workspaces"]:
+            with st.expander("🖥️ **Workspaces**"):
+                # Define workspaces directory outside of repository
+                workspaces_dir = Path("..", "workspaces-" + st.session_state.settings["repository-name"])
+                # Online: show current workspace name in info text and option to change to other existing workspace
+                if st.session_state.location == "local":
+                    # Define callback function to change workspace
+                    def change_workspace():
+                        for key in params.keys():
+                            if key in st.session_state.keys():
+                                del st.session_state[key]
+                        st.session_state.workspace = Path(
+                            workspaces_dir, st.session_state["chosen-workspace"]
+                        )
+                        st.query_params.workspace = st.session_state["chosen-workspace"]
+
+                    # Get all available workspaces as options
+                    options = [
+                        file.name for file in workspaces_dir.iterdir() if file.is_dir()
+                    ]
+                    # Let user chose an already existing workspace
+                    st.selectbox(
+                        "choose existing workspace",
+                        options,
+                        index=options.index(str(st.session_state.workspace.stem)),
+                        on_change=change_workspace,
+                        key="chosen-workspace",
                     )
-                    st.query_params.workspace = st.session_state["chosen-workspace"]
-
-                # Get all available workspaces as options
-                options = [
-                    file.name for file in workspaces_dir.iterdir() if file.is_dir()
-                ]
-                # Let user chose an already existing workspace
-                st.selectbox(
-                    "choose existing workspace",
-                    options,
-                    index=options.index(str(st.session_state.workspace.stem)),
-                    on_change=change_workspace,
-                    key="chosen-workspace",
-                )
-                # Create or Remove workspaces
-                create_remove = st.text_input("create/remove workspace", "")
-                path = Path(workspaces_dir, create_remove)
-                # Create new workspace
-                if st.button("**Create Workspace**"):
-                    path.mkdir(parents=True, exist_ok=True)
-                    st.session_state.workspace = path
-                    st.query_params.workspace = create_remove
-                    # Temporary as the query update takes a short amount of time
-                    time.sleep(1)
-                    st.rerun()
-                # Remove existing workspace and fall back to default
-                if st.button("⚠️ Delete Workspace"):
-                    if path.exists():
-                        shutil.rmtree(path)
-                        st.session_state.workspace = Path(workspaces_dir, "default")
-                        st.query_params.workspace = "default"
+                    # Create or Remove workspaces
+                    create_remove = st.text_input("create/remove workspace", "")
+                    path = Path(workspaces_dir, create_remove)
+                    # Create new workspace
+                    if st.button("**Create Workspace**"):
+                        path.mkdir(parents=True, exist_ok=True)
+                        st.session_state.workspace = path
+                        st.query_params.workspace = create_remove
+                        # Temporary as the query update takes a short amount of time
+                        time.sleep(1)
                         st.rerun()
+                    # Remove existing workspace and fall back to default
+                    if st.button("⚠️ Delete Workspace"):
+                        if path.exists():
+                            shutil.rmtree(path)
+                            st.session_state.workspace = Path(workspaces_dir, "default")
+                            st.query_params.workspace = "default"
+                            st.rerun()
 
         # All pages have settings, workflow indicator and logo
         with st.expander("⚙️ **Settings**"):
@@ -322,6 +341,28 @@ def change_workspace():
                 )
             else:
                 st.session_state["spectrum_num_bins"] = 50
+
+        # Display OpenMS WebApp Template Version from settings.json 
+        with st.container():
+            st.markdown(
+                """
+                <style>
+                .version-box {
+                    border: 1px solid #a4a5ad; 
+                    padding: 10px;
+                    border-radius: 0.5rem;
+                    text-align: center;
+                    display: flex;
+                    justify-content: center;
+                    align-items: center; 
+                }
+                </style>
+                """,
+                unsafe_allow_html=True
+            )
+            version_info = st.session_state.settings["version"] 
+            app_name = st.session_state.settings["app-name"] 
+            st.markdown(f'<div class="version-box">{app_name}<br>Version: {version_info}</div>', unsafe_allow_html=True)
     return params
 
 

src/view.py

@@ -35,6 +35,10 @@ def get_df(file: Union[str, Path]) -> pd.DataFrame:
         else:
             precs.append(np.nan)
     df_spectra["precursor m/z"] = precs
+
+    # Drop spectra without peaks
+    df_spectra = df_spectra[df_spectra["mzarray"].apply(lambda x: len(x) > 0)]
+
     df_spectra["max intensity m/z"] = df_spectra.apply(
         lambda x: x["mzarray"][x["intarray"].argmax()], axis=1
     )
@@ -75,13 +79,13 @@ def plot_bpc_tic() -> go.Figure:
         fig = df.plot(
             backend="ms_plotly",
             kind="chromatogram",
-            fig=fig,
             x="RT",
             y="inty",
             by="type",
-            line_color="#f24c5c",
+            color="#f24c5c",
             show_plot=False,
             grid=False,
+            aggregate_duplicates=True,
         )
     if st.session_state.view_bpc:
         df = st.session_state.view_ms1.groupby("RT").max().reset_index()
@@ -91,13 +95,13 @@ def plot_bpc_tic() -> go.Figure:
         fig = df.plot(
             backend="ms_plotly",
             kind="chromatogram",
-            fig=fig,
             x="RT",
             y="inty",
             by="type",
-            line_color="#2d3a9d",
+            color="#2d3a9d",
             show_plot=False,
             grid=False,
+            aggregate_duplicates=True,
         )
     if st.session_state.view_eic:
         df = st.session_state.view_ms1
@@ -111,21 +115,21 @@ def plot_bpc_tic() -> go.Figure:
             df_eic = df[
                 (df["mz"] >= target_value - tolerance)
                 & (df["mz"] <= target_value + tolerance)
-            ]
+            ].copy()
             if not df_eic.empty:
-                df_eic["type"] = "XIC"
+                df_eic.loc[:, "type"] = "XIC"
                 if df_eic["inty"].max() > max_int:
                     max_int = df_eic["inty"].max()
                 fig = df_eic.plot(
                     backend="ms_plotly",
                     kind="chromatogram",
-                    fig=fig,
                     x="RT",
                     y="inty",
                     by="type",
-                    line_color="#f6bf26",
+                    color="#f6bf26",
                     show_plot=False,
                     grid=False,
+                    aggregate_duplicates=True,
                 )
         except ValueError:
             st.error("Invalid m/z value for XIC provided. Please enter a valid number.")
@@ -149,12 +153,13 @@ def plot_ms_spectrum(df, title, bin_peaks, num_x_bins):
         backend="ms_plotly",
         x="mz",
         y="intensity",
-        line_color="#2d3a9d",
+        color="#2d3a9d",
         title=title,
         show_plot=False,
         grid=False,
         bin_peaks=bin_peaks,
         num_x_bins=num_x_bins,
+        aggregate_duplicates=True,
     )
     fig.update_layout(
         template="plotly_white", dragmode="select", plot_bgcolor="rgb(255,255,255)"
@@ -183,6 +188,7 @@ def view_peak_map():
         show_plot=False,
         bin_peaks=True,
         backend="ms_plotly",
+        aggregate_duplicates=True,
     )
     peak_map.update_layout(template="simple_white", dragmode="select")
     c1, c2 = st.columns(2)
@@ -212,6 +218,7 @@ def view_peak_map():
                 num_x_bins=st.session_state.spectrum_num_bins,
                 height=650,
                 width=900,
+                aggregate_duplicates=True,
             )
             st.plotly_chart(peak_map_3D, use_container_width=True)