prune md readme and add link to release

Author: nikohansen

README.md

@@ -63,7 +63,7 @@ The implementation of the two-objective archive is heavily based on the [`bisect
 
 
 ## Releases
-- 1.0.0 addition of MOArchive classes for 3 and 4 objectives, as well as a class for handling solutions to constrained problems
+- [1.0.0](https://github.com/CMA-ES/moarchiving/releases/tag/r1.0.0) addition of MOArchive classes for 3 and 4 objectives, as well as a class for handling solutions to constrained problems
 - 0.7.0 reimplementation of `BiobjectiveNondominatedSortedList.hypervolume_improvement` by extracting a sublist first.
 - 0.6.0 the `infos` attribute is a `list` with corresponding (arbitrary) information, e.g. for keeping the respective solutions.
 - 0.5.3 fixed assertion error when not using `fractions.Fraction`
@@ -302,204 +302,3 @@ print(moa3_nofr.hypervolume)
     15.899999999999999
 
 
-### 11. Additional functions
-MOArchive also implements additional functions to check whether a given point is in the archive:
-- `in_domain`: Is the point in the domain?
-- `dominates`: Is the point dominated by the archive?
-- `dominators`: Which points (and how many) dominate the given point?
-
-
-```python
-points_list = [[5, 5, 0], [2, 2, 3], [0, 2, 3]]
-print("archive:", list(moa), "\n")
-print("point     | in domain | dominates | num of dominators | dominators")
-print("----------|-----------|-----------|-------------------|-----------")
-for point in points_list:
-    print(f"{point} | {moa.in_domain(point):9} | {moa.dominates(point):9} | "
-          f"{moa.dominators(point, number_only=True):17} | {moa.dominators(point)}")
-```
-
-    archive: [[1, 3, 0], [3, 2, 1], [2, 2, 2], [1, 2, 3]] 
-    
-    point     | in domain | dominates | num of dominators | dominators
-    ----------|-----------|-----------|-------------------|-----------
-    [5, 5, 0] |         0 |         1 |                 1 | [[1, 3, 0]]
-    [2, 2, 3] |         1 |         1 |                 2 | [[2, 2, 2], [1, 2, 3]]
-    [0, 2, 3] |         1 |         0 |                 0 | []
-
-
-### 12. Visualization of indicator values
-By saving the values of indicators for each solution added to the archive, we can visualize their change over time.
-
-
-```python
-import matplotlib.pyplot as plt
-import random
-
-n_obj = 3
-
-indicators_cmoa = []
-indicators_moa = []
-cmoa = get_cmo_archive(reference_point=[0.5] * n_obj, n_obj=n_obj, tau=0.2)
-moa = get_mo_archive(reference_point=[0.1] * n_obj, n_obj=n_obj)
-
-for i in range(2000):
-    objectives = [random.random() for _ in range(n_obj)]
-    constraints = [max(random.random() - 0.1, 0), max(random.random() - 0.1, 0)]
-    
-    cmoa.add(objectives, constraints, info=f"point_{i}")
-    moa.add(objectives, info=f"point_{i}")
-    
-    indicators_cmoa.append((cmoa.hypervolume_plus_constr, cmoa.hypervolume_plus, cmoa.hypervolume))
-    indicators_moa.append((moa.hypervolume_plus, moa.hypervolume))
-    
-```
-
-
-```python
-fig, axs = plt.subplots(1, 2, figsize=(10, 5))
-axs[0].plot([x[2] for x in indicators_cmoa], label="hypervolume")
-axs[0].plot([x[1] for x in indicators_cmoa], label="hypervolume_plus")
-axs[0].plot([x[0] for x in indicators_cmoa], label="hypervolume_plus_constr")
-axs[0].axhline(0, color="black", linestyle="--", zorder=0)
-axs[0].axhline(-cmoa.tau, color="black", linestyle="--", zorder=0)
-axs[0].set_title("Constrained MOArchive")
-axs[0].legend()
-
-axs[1].plot([x[1] for x in indicators_moa], label="hypervolume")
-axs[1].plot([x[0] for x in indicators_moa], label="hypervolume_plus")
-axs[1].set_title("MOArchive")
-axs[1].axhline(0, color="black", linestyle="--", zorder=0)
-axs[1].legend()
-plt.show()
-```
-
-
-    
-![png](README_files/README_31_0.png)
-    
-
-
-### 13. Performance tests
-
-
-```python
-import time
-from moarchiving.tests.point_sampling import get_non_dominated_points
-test_archive_sizes = [0] + [2 ** i for i in range(21)]
-
-get_mo_archive.hypervolume_computation_float_type = fractions.Fraction
-get_mo_archive.hypervolume_final_float_type = fractions.Fraction
-```
-
-#### 13.1. Initializing the archive
-
-
-```python
-n_repeats = 100
-time_limit = 10
-
-for n_obj in [2, 3, 4]:
-    print(f"Testing {n_obj} objectives")
-    times = []
-    archive_sizes = []
-    
-    for archive_size in test_archive_sizes:
-        points = get_non_dominated_points(archive_size, n_dim=n_obj)
-        t0 = time.time()
-        moa = [get_mo_archive(points, [1] * n_obj, n_obj=n_obj)
-               for _ in range(n_repeats)]
-        hv = [m.hypervolume for m in moa]
-        t1 = time.time()
-        
-        times.append(max((t1 - t0) / n_repeats, 10e-4))
-        print(".", end="")
-        archive_sizes.append(archive_size)
-        
-        if t1 - t0 > time_limit:
-            break
-    print()
-    
-    plt.plot(archive_sizes, times, '-o', label=f"{n_obj} objectives")
-
-plt.title("Initialization and hypervolume computation")
-plt.xlabel("Archive size")
-plt.ylabel("Time [s]")
-plt.yscale("log")
-plt.xscale("log")
-plt.grid(True)
-plt.legend()
-plt.show()
-```
-
-    Testing 2 objectives
-    ...............
-    Testing 3 objectives
-    .............
-    Testing 4 objectives
-    .........
-
-
-
-    
-![png](README_files/README_35_1.png)
-    
-
-
-#### 13.2. Adding a solution to an existing archive
-
-
-```python
-n_repeats = 10
-time_limit = 10
-
-for n_obj in [2, 3, 4]:
-    print(f"Testing {n_obj} objectives")
-    times = []
-    archive_sizes = []
-
-    for archive_size in test_archive_sizes:
-        
-        points = get_non_dominated_points(archive_size, n_dim=n_obj)
-        add_points = get_non_dominated_points(n_repeats, n_dim=n_obj)
-        moa = [get_mo_archive(points, [1] * n_obj, n_obj=n_obj) for _ in range(n_repeats)]
-        
-        t0 = time.time()
-        for i, m in enumerate(moa):
-            m.add(add_points[i])
-        t1 = time.time()
-
-        times.append(max((t1 - t0) / n_repeats, 10e-4))
-        print(".", end="")
-        archive_sizes.append(archive_size)
-
-        if t1 - t0 > time_limit:
-            break
-    print()
-    time.sleep(1)
-
-    plt.plot(archive_sizes, times, '-o', label=f"{n_obj} objectives")
-
-plt.title("Adding a point to the archive")
-plt.xlabel("Archive size")
-plt.ylabel("Time [s]")
-plt.yscale("log")
-plt.xscale("log")
-plt.grid(True)
-plt.legend()
-plt.show()
-```
-
-    Testing 2 objectives
-    ......................
-    Testing 3 objectives
-    ................
-    Testing 4 objectives
-    ...........
-
-
-
-    
-![png](README_files/README_37_1.png)
-    
-

howto/release.md

@@ -31,11 +31,11 @@ Make distribution
 
 ```sh
     cd install-folder
-    python -c "open('README.md', 'w').write(open('../README.md', 'r').read().split('### 11')[0])"
+    python -c "s = open('../README.md', 'r').read().split('### 11')[0]; open('README.md', 'w').write(s)"
     python -m build > dist_call_output.txt
     less dist_call_output.txt  # not very informative
     ll dist  # just checking creation date
-    tar -tf dist/moarchiving-1.0.0.tar.gz | tree --fromfile  # check that the distribution folders are clean
+    tar -tf dist/moarchiving-1.0.0.tar.gz | tree --fromfile | less  # check that the distribution folders are clean
 ```
 
 Check distribution and project description:

howto/update_readme.md

@@ -1,7 +1,10 @@
-Files `README.md` and `index.html` are created from the notebook `moarchiving.ipynb`
+# How to update readme and index.html files
+
+The files `README.md` and `index.html` are created from the notebook `moarchiving.ipynb`.
 To update the files, make changes in the notebook, and then run the following commands:
 
 ```bash
-jupyter nbconvert --to markdown --output README  moarchiving.ipynb 
 jupyter nbconvert --to html --output index  moarchiving.ipynb 
-```
+ jupyter nbconvert --to markdown --output README  moarchiving.ipynb
+python -c "s = open('README.md', 'r').read().split('### 11')[0]; open('README.md', 'w').write(s)"
+```

index.html

@@ -14620,7 +14620,7 @@ <h2 id="Links">Links<a class="anchor-link" href="#Links">&#182;</a></h2><ul>
 <h2 id="Details">Details<a class="anchor-link" href="#Details">&#182;</a></h2><p><code>moarchiving</code> with 2 objectives uses the <a href="https://docs.python.org/3/library/fractions.html"><code>fractions.Fraction</code></a> type to avoid rounding errors when computing hypervolume differences, but its usage can also be easily switched off by assigning the respective class attributes <code>hypervolume_computation_float_type</code> and <code>hypervolume_final_float_type</code>. The Fraction type can become prohibitively computationally expensive with increasing precision.</p>
 <p>The implementation of the two-objective archive is heavily based on the <a href="https://docs.python.org/3/library/bisect.html"><code>bisect</code></a> module, while in three and four objectives it is based on the <a href="https://pypi.org/project/sortedcontainers/"><code>sortedcontainers</code></a> module.</p>
 <h2 id="Releases">Releases<a class="anchor-link" href="#Releases">&#182;</a></h2><ul>
-<li>1.0.0 addition of MOArchive classes for 3 and 4 objectives, as well as a class for handling solutions to constrained problems</li>
+<li><a href="https://github.com/CMA-ES/moarchiving/releases/tag/r1.0.0">1.0.0</a> addition of MOArchive classes for 3 and 4 objectives, as well as a class for handling solutions to constrained problems</li>
 <li>0.7.0 reimplementation of <code>BiobjectiveNondominatedSortedList.hypervolume_improvement</code> by extracting a sublist first.</li>
 <li>0.6.0 the <code>infos</code> attribute is a <code>list</code> with corresponding (arbitrary) information, e.g. for keeping the respective solutions.</li>
 <li>0.5.3 fixed assertion error when not using <code>fractions.Fraction</code></li>

moarchiving.ipynb

@@ -69,7 +69,7 @@
     "\n",
     "\n",
     "## Releases\n",
-    "- 1.0.0 addition of MOArchive classes for 3 and 4 objectives, as well as a class for handling solutions to constrained problems\n",
+    "- [1.0.0](https://github.com/CMA-ES/moarchiving/releases/tag/r1.0.0) addition of MOArchive classes for 3 and 4 objectives, as well as a class for handling solutions to constrained problems\n",
     "- 0.7.0 reimplementation of `BiobjectiveNondominatedSortedList.hypervolume_improvement` by extracting a sublist first.\n",
     "- 0.6.0 the `infos` attribute is a `list` with corresponding (arbitrary) information, e.g. for keeping the respective solutions.\n",
     "- 0.5.3 fixed assertion error when not using `fractions.Fraction`\n",