Merge pull request #159 from ACCLAB/∆∆_bootstrap_rewrite

Delta2 Bootstrap Function Rewrite, nbdev Configuration and Templates for Bug Report, Feature Request added
ACCLAB · Feb 28, 2024 · 37786a3 · 37786a3
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -0,0 +1,34 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1.  
+2.  
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Your package version (please complete the following information):**
+ - dabest: [e.g. 2023.3.29]
+ - pandas: 
+ - numpy: 
+ - matplotlib:
+ - seaborn:
+ - scipy:
+
+
+**Additional context**
+Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -0,0 +1,23 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Is a dataset available for testing out the functionality**
+If yes, please leave a Google Drive link 
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [email protected]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,23 @@
+# Contributing to DABEST-Python
+
+
+## Did you find a bug?
+- Ensure the bug was not already reported by searching in [Issues](https://github.com/ACCLAB/DABEST-python/issues). Check that the bug hasn't been addressed in a closed issue.
+
+- If the bug isn't being addressed, open a new issue using the Bug report template. Be sure to fill in the necessary information, and a [minimally reproducible code sample](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) demonstrating the expected behavior that is not occurring. 
+
+
+## Did you write a patch that fixes a bug?
+- Open a new GitHub [pull request](https://help.github.com/en/articles/about-pull-requests) (PR for short) with the patch.
+
+- Create the PR into the development branch, which is indicated by `v{latest version number}-dev`.
+
+- Clearly state the problem and solution in the PR description. Include the relevant [issue number](https://guides.github.com/features/issues/) if applicable.
+
+
+## Do you intend to add a new feature or change an existing one?
+- Suggest your change by opening an issue using the Feature request template.
+- If the maintainers and the community are in favour, create a fork and start writing code.
+
+
+DABEST is a community tool for estimation statistics and analysis. We look forward to more robust and more elegant data visualizations from you all!
diff --git a/README.md b/README.md
@@ -84,14 +84,17 @@ obtain the dependencies easily.
 
 You can install this package via `pip`.
 
-To install, at the command line run <!-- ```shell
+To install, at the command line run
+
+``` shell
 conda config --add channels conda-forge
 conda install dabest
 ```
-or -->
+
+or –\>
 
 ``` shell
-pip install --upgrade dabest
+pip install dabest
 ```
 
 You can also
@@ -150,18 +153,19 @@ tracker](https://github.com/ACCLAB/DABEST-python/issues/new).
 ## Contributing
 
 All contributions are welcome; please read the [Guidelines for
-contributing](https://github.com/ACCLAB/DABEST-python/blob/master/CONTRIBUTING.md)
-first.
+contributing](CONTRIBUTING.md) first.
 
-We also have a [Code of
-Conduct](https://github.com/ACCLAB/DABEST-python/blob/master/CODE_OF_CONDUCT.md)
-to foster an inclusive and productive space.
+We also have a [Code of Conduct](CODE_OF_CONDUCT.md) to foster an
+inclusive and productive space.
 
 ### A wish list for new features
 
 If you have any specific comments and ideas for new features that you
-would like to share with us, please fill this form. **Add the link to a
-google doc form**
+would like to share with us, please read the [Guidelines for
+contributing](CONTRIBUTING.md), create a new issue using Feature request
+template or create a new post in [our Google
+Group](https://groups.google.com/g/estimationstats).
+
 
 ## Acknowledgements
 
@@ -175,12 +179,20 @@ Stanislav Ott.
 ## Testing
 
 To test DABEST, you need to install
-[pytest](https://docs.pytest.org/en/latest).
 
-Run `pytest` in the root directory of the source distribution. This runs
-the test suite in the folder `dabest/tests`. The test suite ensures that
-the bootstrapping functions and the plotting functions perform as
-expected.
+[pytest](https://docs.pytest.org/en/latest) and
+[nbdev](https://nbdev.fast.ai/).
+
+- Run `pytest` in the root directory of the source distribution. This
+  runs the test suite in the folder `dabest/tests/mpl_image_tests`.
+- Run `nbdev_test` in the root directory of the source distribution.
+  This runs the value assertion tests in parent folder `dabest/tests`
+
+The test suite ensures that the bootstrapping functions and the plotting
+functions perform as expected.
+
+For detailed information, please refer to the [test
+folder](nbs/tests/README.md)
 
 ## DABEST in other languages
 

diff --git a/dabest/_modidx.py b/dabest/_modidx.py
@@ -2,8 +2,8 @@
 
 d = { 'settings': { 'branch': 'master',
                 'doc_baseurl': '/DABEST-python',
-                'doc_host': 'https://ZHANGROU-99.github.io',
-                'git_url': 'https://github.com/ZHANGROU-99/DABEST-python',
+                'doc_host': 'https://acclab.github.io',
+                'git_url': 'https://github.com/acclab/DABEST-python',
                 'lib_path': 'dabest'},
   'syms': { 'dabest._stats_tools.confint_1group': { 'dabest._stats_tools.confint_1group.compute_1group_acceleration': ( 'API/confint_1group.html#compute_1group_acceleration',
                                                                                                                         'dabest/_stats_tools/confint_1group.py'),

diff --git a/dabest/_stats_tools/confint_2group_diff.py b/dabest/_stats_tools/confint_2group_diff.py
@@ -155,74 +155,57 @@ def compute_delta2_bootstrapped_diff(
     """
 
     rng = RandomState(PCG64(random_seed))
-    x1_len = len(x1)
-    x2_len = len(x2)
-    x3_len = len(x3)
-    x4_len = len(x4)
-    out_delta_g = np.repeat(np.nan, resamples)
-    deltadelta = np.repeat(np.nan, resamples)
-
-    n_a1_b1, n_a2_b1, n_a1_b2, n_a2_b2 = x1_len, x2_len, x3_len, x4_len
-    s_a1_b1, s_a2_b1, s_a1_b2, s_a2_b2 = np.std(x1), np.std(x2), np.std(x3), np.std(x4)
-
-    sd_numerator = (
-        (n_a2_b1 - 1) * s_a2_b1**2
-        + (n_a1_b1 - 1) * s_a1_b1**2
-        + (n_a2_b2 - 1) * s_a2_b2**2
-        + (n_a1_b2 - 1) * s_a1_b2**2
-    )
-    sd_denominator = (n_a2_b1 - 1) + (n_a1_b1 - 1) + (n_a2_b2 - 1) + (n_a1_b2 - 1)
+
+    x1, x2, x3, x4 = map(np.asarray, [x1, x2, x3, x4])
+
+    # Calculating pooled sample standard deviation
+    stds = [np.std(x) for x in [x1, x2, x3, x4]]
+    ns = [len(x) for x in [x1, x2, x3, x4]]
+
+    sd_numerator = sum((n - 1) * s**2 for n, s in zip(ns, stds))
+    sd_denominator = sum(n - 1 for n in ns)
+
+    # Avoid division by zero
+    if sd_denominator == 0:
+        raise ValueError("Insufficient data to compute pooled standard deviation.")
+
     pooled_sample_sd = np.sqrt(sd_numerator / sd_denominator)
 
-    for i in range(int(resamples)):
+    # Ensure pooled_sample_sd is not NaN or zero (to avoid division by zero later)
+    if np.isnan(pooled_sample_sd) or pooled_sample_sd == 0:
+        raise ValueError("Pooled sample standard deviation is NaN or zero.")
+
+    out_delta_g = np.empty(resamples)
+    deltadelta = np.empty(resamples)
+
+    # Bootstrapping
+    for i in range(resamples):
+        # Paired or unpaired resampling
         if is_paired:
-            if (x1_len != x2_len) or (x3_len != x4_len):
-                raise ValueError("The two arrays do not have the same length.")
-            df_paired_1 = pd.DataFrame(
-                {
-                    "value": np.concatenate([x1, x3]),
-                    "array_id": np.repeat(["x1", "x3"], [x1_len, x3_len]),
-                }
-            )
-            df_paired_2 = pd.DataFrame(
-                {
-                    "value": np.concatenate([x2, x4]),
-                    "array_id": np.repeat(["x2", "x4"], [x1_len, x3_len]),
-                }
-            )
-            x_sample_index = rng.choice(
-                len(df_paired_1), len(df_paired_1), replace=True
-            )
-            x_sample_1 = df_paired_1.loc[x_sample_index]
-            x_sample_2 = df_paired_2.loc[x_sample_index]
-            x1_sample = x_sample_1[x_sample_1["array_id"] == "x1"]["value"]
-            x2_sample = x_sample_2[x_sample_2["array_id"] == "x2"]["value"]
-            x3_sample = x_sample_1[x_sample_1["array_id"] == "x3"]["value"]
-            x4_sample = x_sample_2[x_sample_2["array_id"] == "x4"]["value"]
+            if len(x1) != len(x2) or len(x3) != len(x4):
+                raise ValueError("Each control group must have the same length as its corresponding test group in paired analysis.")
+            indices_1 = rng.choice(len(x1), len(x1), replace=True)
+            indices_2 = rng.choice(len(x3), len(x3), replace=True)
+
+            x1_sample, x2_sample = x1[indices_1], x2[indices_1]
+            x3_sample, x4_sample = x3[indices_2], x4[indices_2]
         else:
-            df = pd.DataFrame(
-                {
-                    "value": np.concatenate([x1, x2, x3, x4]),
-                    "array_id": np.repeat(
-                        ["x1", "x2", "x3", "x4"], [x1_len, x2_len, x3_len, x4_len]
-                    ),
-                }
-            )
-            x_sample_index = rng.choice(len(df), len(df), replace=True)
-            x_sample = df.loc[x_sample_index]
-            x1_sample = x_sample[x_sample["array_id"] == "x1"]["value"]
-            x2_sample = x_sample[x_sample["array_id"] == "x2"]["value"]
-            x3_sample = x_sample[x_sample["array_id"] == "x3"]["value"]
-            x4_sample = x_sample[x_sample["array_id"] == "x4"]["value"]
+            x1_sample = rng.choice(x1, len(x1), replace=True)
+            x2_sample = rng.choice(x2, len(x2), replace=True)
+            x3_sample = rng.choice(x3, len(x3), replace=True)
+            x4_sample = rng.choice(x4, len(x4), replace=True)
 
+        # Calculating deltas
         delta_1 = np.mean(x2_sample) - np.mean(x1_sample)
         delta_2 = np.mean(x4_sample) - np.mean(x3_sample)
         delta_delta = delta_2 - delta_1
+
         deltadelta[i] = delta_delta
         out_delta_g[i] = delta_delta / pooled_sample_sd
-    delta_g = (
-        (np.mean(x4) - np.mean(x3)) - (np.mean(x2) - np.mean(x1))
-    ) / pooled_sample_sd
+
+    # Empirical delta_g calculation
+    delta_g = ((np.mean(x4) - np.mean(x3)) - (np.mean(x2) - np.mean(x1))) / pooled_sample_sd
+
     return out_delta_g, delta_g, deltadelta
 
 

diff --git a/nbs/01-getting_started.ipynb b/nbs/01-getting_started.ipynb
@@ -75,7 +75,7 @@
     "Clone the [DABEST-python repo](https://github.com/ACCLAB/DABEST-python) locally (see instructions [here](https://help.github.com/articles/cloning-a-repository/)).\n",
     "\n",
     "Then, navigate to the cloned repo in the command line and run\n",
-    "```\n",
+    "``` shell\n",
     "$ pip install .\n",
     "```"
    ]
@@ -93,9 +93,13 @@
    "id": "a9f8cb3e",
    "metadata": {},
    "source": [
-    "To test DABEST, you will need to install [pytest](https://docs.pytest.org/en/latest/). \n",
+    "To test DABEST, you will need to install [pytest](https://docs.pytest.org/en/latest/) and [nbdev](https://nbdev.fast.ai/). \n",
+    "\n",
+    "Run ``nbdev_export && nbdev_test`` in the root directory of the source distribution. This runs the value assertion tests in ``dabest/tests`` folder\n",
+    "\n",
+    "Run ``pytest`` in the root directory of the source distribution. This runs the image-based tests in ``dabest/tests/mpl_image_tests`` sub folder.\n",
     "\n",
-    "Run ``pytest`` in the root directory of the source distribution. This runs the test suite in ``dabest/tests`` folder including also the image-based tests of the ``mpl_image_tests`` sub folder. The test suite will ensure that the bootstrapping functions and the plotting functions perform as expected.\n",
+    "The test suite will ensure that the bootstrapping functions and the plotting functions perform as expected.\n",
     "\n"
    ]
   },