Improve install and results generation process

.gitignore

@@ -10,8 +10,8 @@ _plots_test/
 _data/
 _results/*.log
 _results/**/*.pkl
-_results_final/
-_results_server/
+_results/
+_results_test/
 
 *.egg-info/
 *.pdf

README.md

@@ -14,7 +14,7 @@ A pre-print is available at [https://arxiv.org/abs/2209.04266](https://arxiv.org
 
 ## Installation
 
-This code was written for Ubuntu 20.04.5, using Python 3.8.10.
+This code was last tested with Ubuntu 20.04.1, using Python 3.10.3
 
 ### Local install
 
@@ -26,29 +26,34 @@ git clone --recursive [email protected]:utiasASRL/safe_and_smooth
 All requirements can be installed by running
 ```
 conda env create -f environment.yml
-conda activate safeandsmooth
 ```
 
 To check that the installation was successful, run
 ```
+conda activate safeandsmooth
 pytest .
 ```
+You can also check that you can generate some toy example results by running
+```
+_scripts/generate_test_results.sh
+```
+and then checking the output created in `_plots_test`. 
 
 Please report any installation issues. 
 
 ## Generate results
 
 There are three types of results reported in the paper:
 
-- Noise study: Run `simulate_noise.py` to generate the simulation study (Figures 4 and 7 (appendix)). 
-- Timing study:  Run `simulate_time.py` to generate the runtime comparison (Figure 5)
-- Real data: Run `evaluate_data.py` to evaluate the real dataset (Figures 1, 5 and 6). 
+- Noise study: Run `_scripts/simulate_noise.py` to generate the simulation study (Figures 4 and 7 (appendix)). 
+- Timing study:  Run `_scripts/simulate_time.py` to generate the runtime comparison (Figure 5)
+- Real data: Run `_scripts/evaluate_real.py` to evaluate the real dataset (Figures 1, 5 and 6). 
 
 You can generate all results by running
 ```
 _scripts/generate_all_results.sh
 ```
-After generating, all data can be evaluated, and new figures created, using the jupyter notebook `SafeAndSmooth.ipynb`. For more evaluations of the real dataset, refer to the notebook `DatasetEvaluation.ipynb`. 
+After generating, all data can be evaluated, and new figures created, by running `python _scripts/plot_results.py`. For more evaluations of the real dataset, refer to the notebook `_notebooks/DatasetEvaluation.ipynb` (you may need to run `pip install -r requirements.txt` for additional plotting libraries). 
 
 ## Code references
 

_scripts/evaluate_real.py

@@ -168,11 +168,8 @@ def evaluate_datasets(
     from utils.helper_params import logs_to_file, parse_arguments
 
     save_results = True
-    out_dir = "_results_final/"
-
     args = parse_arguments("Generate dataset results.")
-    if args.test:
-        out_dir = "_results/"
+    out_dir = args.resultdir
 
     logfile = os.path.join(out_dir, "evaluate_real.log")
     with logs_to_file(logfile):

_scripts/generate_all_results.sh

@@ -1,13 +1,5 @@
 #!/bin/bash
-
-# run with fewer instances to make sure everything is working properly.
-#python3 _scripts/simulate_time.py --test --resultdir="_results"
-#python3 _scripts/simulate_noise.py --test --resultdir="_results"
-#python3 _scripts/evaluate_real.py --test --resultdir="_results"
-python3 _scripts/plot_results.py --resultdir="_results_server" --plotdir="_plots_test/"
-
-# generate final results
-#python3 _scripts/simulate_time.py --resultdir="_results_final/"
-#python3 _scripts/simulate_noise.py --resultdir="_results_final/"
-#python3 _scripts/evaluate_real.py --resultdir="_results_final/"
-#python3 _scripts/plot_results.py --resultdir="_results_final/" --plotdir="_plots/"
+#python3 _scripts/simulate_time.py --resultdir="_results"
+#python3 _scripts/simulate_noise.py --resultdir="_results"
+python3 _scripts/evaluate_real.py --resultdir="_results"
+python3 _scripts/plot_results.py --resultdir="_results" --plotdir="_plots"

_scripts/generate_test_results.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+# run with fewer instances to make sure everything is working properly.
+#python3 _scripts/simulate_time.py --test --resultdir="_results_test"
+#python3 _scripts/simulate_noise.py --test --resultdir="_results_test"
+python3 _scripts/evaluate_real.py --test --resultdir="_results_test"
+python3 _scripts/plot_results.py --resultdir="_results_test" --plotdir="_plots_test"

_scripts/plot_results.py

@@ -679,12 +679,12 @@ def plot_real_top_calib(outdir, plotdir):
     from utils.helper_params import parse_arguments
 
     args = parse_arguments("Plot all results")
+    plot_real_top_calib(args.resultdir, args.plotdir)
 
     plot_noise(args.resultdir, args.plotdir)
     plot_timing(args.resultdir, args.plotdir)
 
     plot_real_top(args.resultdir, args.plotdir)
-    plot_real_top_calib(args.resultdir, args.plotdir)
     plot_real_top_estimate(args.resultdir, args.plotdir)
 
     plot_problem_setup(args.plotdir)

_scripts/simulate_noise.py

@@ -177,8 +177,8 @@ def generate_results(params_dir, out_dir, save_results=SAVE_RESULTS, test=False)
             if save_results:
                 results.to_pickle(fname)
                 print("saved intermediate as", fname)
-    if test:
-        plt.show()
+    # if test:
+    #    plt.show()
     return results
 
 

environment.yml

@@ -7,16 +7,6 @@ dependencies:
     - python=3.10
     - pip=22.3
 
-    - jupyter
-    - seaborn>=0.12.2
-    - numpy>=1.23.5
-    - scipy==1.10.0
-    - pandas>=1.4.3
-    - plotly>=5.18.0
-    - progressbar2==4.0
-    - pyyaml>=6.0
-    - pytest>=7.1.2
-
     - pip:
       - -e poly_matrix
       - -e . 

requirements.txt

@@ -1,10 +1,9 @@
-jupyter
-seaborn>=0.12.2
 numpy>=1.23.5
-scipy>=1.9.0
+scipy==1.10.0
+matplotlib>=3.8.1
 pandas>=1.4.3
 progressbar2==4.0
 pyyaml>=6.0
 pytest>=7.1.2
-scikit-umfpack>=0.3.3
-scikit-sparse>=0.4.8
+jupyter
+plotly>=5.18.0

setup.cfg

@@ -14,11 +14,19 @@ license = { file="LICENSE" }
 
 [options]
 packages = find:
+python_requires = >=3.10
+install_requires =
+  numpy
+  scipy
+  matplotlib
+  pandas
+  progressbar2
+  pyyaml
 
 [options.packages.find] # do not mistake tests/ for a package directory
 exclude=tests*
 
 [flake8]
-ignore = W292, W391, F541, F841, W503 
+ignore = W292, W391, F541, F841, W503, E741
 exclude = _notebooks/*, *.ipynb_checkpoints*
 max-line-length = 99

utils/helper_params.py

@@ -80,7 +80,7 @@ def parse_arguments(description=""):
         "-r",
         "--resultdir",
         help="directory of results",
-        default="_results",
+        default="_results_test",
     )
     parser.add_argument(
         "-p",