forgot to include all files

.github/workflows/build_docker.yml

@@ -129,7 +129,7 @@ jobs:
             ln -s ../configs/chr202122_run/sampler_per_window configs
             python ~/ont_project_all/ont_project/usecases/enrich_usecase.py
 
-            tar -cvzf figures.tar.gz readfish_run/figures
+            tar -cvzf figures.tar.gz simulator_run/figures
       - 
         name: Archive figures
         uses: actions/upload-artifact@v3

README.md

@@ -9,7 +9,53 @@ This repository provides a simulator for an ONT device controlled by the ReadUnt
 The code is well-tested with `pytest` and an example usecase combining the simulator with ReadFish and NanoSim is provided.
 Access the documentation [here](https://ratschlab.github.io/sim_read_until/).
 
-See below for a [quick start](#quick-start).
+A video for the CLI interface of the simulator (as described in [usecases](usecases/README.md)) is available here: [CLI interface Youtube](https://youtu.be/8GDTD4Memes)
+See below for an [overview](#overview).
+
+## Quick Start
+
+Clone the repository, install the virtual environment and run the usecase, as explained below.
+
+### Installation and Setup
+
+We have tested the code with python3.10 and python3.8 on Linux and Mac OS X, so try to use it:
+```{bash}
+# create a shared directory:
+mkdir ~/ont_project_all
+cd ~/ont_project_all
+
+git clone --depth 1 [email protected]:ratschlab/sim_read_until.git ont_project
+# the NanoSim repository (integrated as a submodule here) is quite large (2Gb) due to pre-computed models, so we omit it here
+# if you want it, do: git clone --recurse-submodules [email protected]:ratschlab/sim_read_until.git ont_project
+
+# conda deactivate # if you have a conda environment activated, including base env
+python3.10 -m venv ont_project_venv
+source ~/ont_project_all/ont_project_venv/bin/activate
+pip install --upgrade pip
+pip install ont_project/
+pip install --upgrade seaborn
+```
+
+Take a look at the directory [usecase](usecases/) to run some example usecases.
+
+If the installation fails due to dependency issues, you can alternatively run it as a Docker image that comes with the dependencies and runs Jupyter lab:
+```{bash}
+# to update the Docker image if a new one was published
+# note: it may not always be up-to-date with the main branch, check the release date online
+docker pull ghcr.io/ratschlab/sim_read_until:main_dev
+
+cd ~/ont_project_all
+./ont_project/start_docker_container.sh
+# to see the options
+# ./ont_project/start_docker_container.sh -h
+```
+Several Docker containers can run in parallel, provided you modify the port and container name via the options `-n` and `-p`.
+
+**Note**: Conda is not officially supported, but you can set up your environment with:
+```{bash}
+conda create -y -n ont_project_venv python=3.10 pip
+```
+Some scripts activate the virtual environment, so you have to change it to `conda activate ont_project_venv`.
 
 ## Overview
 
@@ -57,52 +103,7 @@ The repository contains the following directories (as submodules):
 - `runs`: for local runs; in `.gitignore`
 - `apidocs`: location for API docs; in `.gitignore`
 
-## Quick Start
-
-Clone the repository, install the virtual environment and run the usecase, as explained below.
-
-### Installation and Setup
-
-We have tested the code with python3.10 and python3.8, so try to use it:
-```{bash}
-# create a shared directory:
-mkdir ~/ont_project_all
-cd ~/ont_project_all
-
-git clone --depth 1 [email protected]:ratschlab/sim_read_until.git ont_project
-# the NanoSim repository (integrated as a submodule here) is quite large (2Gb) due to pre-computed models, so we omit it here
-# if you want it, do: git clone --recurse-submodules [email protected]:ratschlab/sim_read_until.git ont_project
-
-# conda deactivate # if you have a conda environment activated, including base env
-python3.10 -m venv ont_project_venv
-source ~/ont_project_all/ont_project_venv/bin/activate
-pip install --upgrade pip
-pip install ont_project/
-pip install --upgrade seaborn
-```
-
-Take a look at the directory [usecase](usecases/) to run some example usecases.
-
-If the installation fails due to dependency issues, you can alternatively run it as a Docker image that comes with the dependencies and runs Jupyter lab:
-```{bash}
-# to update the Docker image if a new one was published
-# note: it may not always be up-to-date with the main branch, check the release date online
-docker pull ghcr.io/ratschlab/sim_read_until:main_dev
-
-cd ~/ont_project_all
-./ont_project/start_docker_container.sh
-# to see the options
-# ./ont_project/start_docker_container.sh -h
-```
-Several Docker containers can run in parallel, provided you modify the port and container name via the options `-n` and `-p`.
-
-**Note**: Conda is not officially supported, but you can set up your environment with:
-```{bash}
-conda create -y -n ont_project_venv python=3.10 pip
-```
-Some scripts activate the virtual environment, so you have to change it to `conda activate ont_project_venv`.
-
-### Comparison with UNCALLED
+## Comparison with UNCALLED
 
 We tried comparing with UNCALLED, but it didn't work due to a segmentation fault without any useful error message, see [uncalled_comparison](uncalled_comparison.md) for details.
 According to the authors, the UNCALLED simulator is superseeded by the recent tool Icarust, which is a tool that addresses a similar setting as we do.

pyproject.toml

@@ -81,6 +81,7 @@ usecase_generate_random_reads = "simreaduntil.usecase_helpers.cli_usecase.genera
 simulator_server_cli = "simreaduntil.usecase_helpers.cli_usecase.simulator_server_cli:main"
 usecase_simulator_client_cli = "simreaduntil.usecase_helpers.cli_usecase.simulator_client_cli:main"
 sim_plots_cli = "simreaduntil.usecase_helpers.cli_usecase.sim_plots_cli:main"
+usecase_make_html_report = "simreaduntil.usecase_helpers.cli_usecase.make_html_report:main"
 
 
 [project.urls]

src/simreaduntil/usecase_helpers/cli_usecase/make_html_report.py

@@ -0,0 +1,102 @@
+"""
+Make an overview page from all figures in the directory
+"""
+import argparse
+import logging
+from pathlib import Path
+import sys
+from simreaduntil.shared_utils.logging_utils import add_comprehensive_stream_handler_to_logger, setup_logger_simple
+from simreaduntil.shared_utils.utils import print_args
+
+logger = setup_logger_simple(__name__)
+"""module logger"""
+
+mainpage_template = r"""
+<!DOCTYPE html>
+<html>
+  <head>
+    <title>Generated Figures</title>
+  </head>
+  <style>
+    img {
+      display: inline-block;
+      margin: 5px;
+      max-width: 100%;
+      max-height: 400px;
+      text-align: center;
+    }
+    
+  </style>
+  <body>
+    <h1>Generated Figures</h1>
+    
+    {FIGURES_HTML}
+
+  </body>
+</html>
+"""
+figure_template = r"""
+<h2 class="image-name">{figure_name}</h2>
+    <div class="photo">
+      <img src="{figure_filename}">
+    </div>
+    <hr style="height:2px;border-width:0;color:gray;background-color:gray">
+    
+"""
+
+def parse_args(args=None):
+    parser = argparse.ArgumentParser(description="Combine images into html report")
+    parser.add_argument("figure_dir", type=Path, help="Directory containing figures (.png files)")
+
+    args = parser.parse_args(args)
+    print_args(args, logger=logger)
+    return args
+
+def main():
+    log_level = logging.DEBUG
+    logging.getLogger(__name__).setLevel(log_level) # log level of this script (running as __main__)
+    add_comprehensive_stream_handler_to_logger(None, level=log_level)
+
+    args = parse_args()
+
+    figure_dir = args.figure_dir
+    assert figure_dir.exists(), f"figure_dir '{figure_dir}' does not exist"
+
+    figure_htmls = ""
+    for filename in figure_dir.glob("*.png"):
+        logger.info(f"Adding '{filename}'")
+        # using relative path wrt to final file!
+        figure_htmls += figure_template.format(figure_name=filename.name, figure_filename=filename.name)
+
+    html_filename = figure_dir / "figures.html"
+    with open(html_filename, "w") as f:
+        f.write(mainpage_template.replace("{FIGURES_HTML}", figure_htmls))
+
+
+# template
+# <!DOCTYPE html>
+# <html>
+#   <head>
+#     <title>Generated Figures</title>
+#   </head>
+#   <style>
+#     img {
+#       display: inline-block;
+#       margin: 5px;
+#       width: 100%;
+#       max-height: 400px;
+#       text-align: center;
+#     }
+
+#   </style>
+#   <body>
+#     <h1>Generated Figures</h1>
+
+#     <h2 class="image-name">nb_basepairs_recrej_per_channel.png</h2>
+#     <div class="photo">
+#       <img src="figures/nb_basepairs_recrej_per_channel.png">
+#     </div>
+#     <hr style="height:2px;border-width:0;color:gray;background-color:gray">
+
+#   </body>
+# </html>

tests/simulator/test_simulator.py

@@ -7,6 +7,7 @@
 import numpy as np
 import matplotlib.pyplot as plt
 import dill
+from simreaduntil.shared_utils.merge_axes import save_fig_and_pickle
 
 from simreaduntil.shared_utils.timing import cur_ns_time
 from simreaduntil.simulator import channel
@@ -215,6 +216,7 @@ def test_random_ops_synchronous(simulator, async_mode, channel_write_zero_length
     # make all elements roughly the same length, reads have length 8-17 -> take about 1.2s
     sim_params = SimParams(
         gap_samplers={f"channel_{i}": ConstantGapsUntilBlocked(short_gap_length=1.2, long_gap_length=1.2, prob_long_gap=0.35, time_until_blocked=200, read_delay=0) for i in range(2)},
+        # gap_samplers={f"channel_{i}": ConstantGapsUntilBlocked(short_gap_length=1.2, long_gap_length=5.2, prob_long_gap=0.25, time_until_blocked=200, read_delay=0) for i in range(2)},
         bp_per_second=10, chunk_size=4, default_unblock_duration=1.2, seed=0,
     )
 
@@ -249,7 +251,7 @@ def get_read_and_save_id():
         if nb_actions["forward"] > 0:
             pass
             # print(1)
-            # ax = simulator.plot_channels(); import matplotlib.pyplot as plt; plt.show(block=True); save_fig_and_pickle(ax.figure, "simulator_example.png");  #note: for README.md figure, zoom into appropriate region, then save the figure, keep it commented out
+            # ax = simulator.plot_channels(); import matplotlib.pyplot as plt; plt.show(block=True); #save_fig_and_pickle(ax.figure, "simulator_example.png");  #note: for README.md figure, zoom into appropriate region, then save the figure, keep it commented out
 
         simulator.stop() if async_mode else simulator.sync_stop()
         check_simulator_actions_agree_with_reads_writer(simulator, cum_nb_actions, check_nb_rejected=(j==0))

tests/simulator/test_simulator_server.py

@@ -103,7 +103,7 @@ def test_launchable_device_grpc_server():
 
             stub.GetActionResults(ont_device_pb2.ActionResultsRequest(clear=True))
 
-            assert stub.StartSim(ont_device_pb2.StartRequest(acceleration_factor=2)).value
+            assert stub.StartSim(ont_device_pb2.StartRequest(acceleration_factor=2, update_method="realtime", log_interval=10)).value
 
             # unblocking inexistent read
             assert not stub.PerformActions(ont_device_pb2.ReadActionsRequest(actions=[