Changes in several documentations

Author: Jacobluke-

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 joseshowh@gmail.com. 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

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 one. Be sure to include a title and clear description, 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, and adding an Enhancement tag. 
+- 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!

README.md

@@ -53,21 +53,21 @@ DABEST is a package for **D**ata **A**nalysis using
 **B**ootstrap-Coupled **EST**imation.
 
 [Estimation
-statistics](https://en.wikipedia.org/wiki/Estimation_statistics) is a
+statistics](https://en.wikipedia.org/wiki/Estimation_statistics) are a
 [simple framework](https://thenewstatistics.com/itns/) that avoids the
 [pitfalls](https://www.nature.com/articles/nmeth.3288) of significance
-testing. It uses familiar statistical concepts: means, mean differences,
-and error bars. More importantly, it focuses on the effect size of one’s
-experiment/intervention, as opposed to a false dichotomy engendered by
-*P* values.
+testing. It employs familiar statistical concepts such as means, mean
+differences, and error bars. More importantly, it focuses on the effect
+size of one’s experiment or intervention, rather than succumbing to a
+false dichotomy engendered by *P* values.
 
-An estimation plot has two key features.
+An estimation plot comprises two key features.
 
-1.  It presents all datapoints as a swarmplot, which orders each point
-    to display the underlying distribution.
+1.  It presents all data points as a swarm plot, ordering each point to
+    display the underlying distribution.
 
-2.  It presents the effect size as a **bootstrap 95% confidence
-    interval** on a **separate but aligned axes**.
+2.  It illustrates the effect size as a **bootstrap 95% confidence
+    interval** on a **separate but aligned axis**.
 
 ![The five kinds of estimation
 plots](showpiece.png "The five kinds of estimation plots.")
@@ -77,21 +77,24 @@ allowing everyone access to high-quality estimation plots.
 
 ## Installation
 
-This package is tested on Python 3.6, 3.7, and 3.8. It is highly
+This package is tested on Python 3.6, 3.7, 3.8 and 3.10. It is highly
 recommended to download the [Anaconda
 distribution](https://www.continuum.io/downloads) of Python in order to
 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
@@ -110,7 +113,7 @@ pip install .
 import pandas as pd
 import dabest
 
-# Load the iris dataset. Requires internet access.
+# Load the iris dataset. This step requires internet access.
 iris = pd.read_csv("https://github.com/mwaskom/seaborn-data/raw/master/iris.csv")
 
 # Load the above data into `dabest`.
@@ -150,50 +153,16 @@ 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
 
-Currently, DABEST offers functions to handle data traditionally analyzed
-with Student’s paired and unpaired t-tests. It also offers plots for
-multiplexed versions of these, and the estimation counterpart to a 1-way
-analysis of variance (ANOVA), the shared-control design. While these
-five functions execute a large fraction of common biomedical data
-analyses, there remain three others: 2-way data, time-series group data,
-and proportional data. We aim to add these new functions to both the R
-and Python libraries.
-
-- In many experiments, four groups are investigate to isolate an
-  interaction, for example: a genotype × drug effect. Here, wild-type
-  and mutant animals are each subjected to drug or sham treatments; the
-  data are traditionally analysed with a 2×2 ANOVA. We have received
-  requests by email, Twitter, and GitHub to implement an estimation
-  counterpart to the 2-way ANOVA. To do this, we will implement
-  $\Delta\Delta$ plots, in which the difference of means ($\Delta$) of
-  two groups is subtracted from a second two-group $\Delta$.
-  **Implemented in v2023.02.14.**
-
-- Currently, DABEST can analyse multiple paired data in a single plot,
-  and multiple groups with a common, shared control. However, a common
-  design in biomedical science is to follow the same group of subjects
-  over multiple, successive time points. An estimation plot for this
-  would combine elements of the two other designs, and could be used in
-  place of a repeated-measures ANOVA. **Implemented in v2023.02.14**
-
-- We have observed that proportional data are often analyzed in
-  neuroscience and other areas of biomedical research. However, compared
-  to other data types, the charts are frequently impoverished: often,
-  they omit error bars, sample sizes, and even P values—let alone effect
-  sizes. We would like DABEST to feature proportion charts, with error
-  bars and a curve for the distribution of the proportional differences.
-  **Implemented in v2023.02.14**
-
-We encourage contributions for the above features.
+If you have any specific comments and ideas for new features that you
+would like to share with us, please fill this
+[form](https://docs.google.com/forms/d/1XnF-dkPFUYDPxH9WNXK0L2uU0uv2ZDy4paiCJuk_Kn0).
 
 ## Acknowledgements
 
@@ -206,13 +175,20 @@ Stanislav Ott.
 
 ## Testing
 
-To test DABEST, you will need to install
-[pytest](https://docs.pytest.org/en/latest).
+To test DABEST, you need to install
+[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.
 
-Run `pytest` in the root directory of the source distribution. This runs
-the test suite in the folder `dabest/tests`. The test suite will ensure
-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
 

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"
    ]
   },

nbs/blog/posts/robust-beautiful/four_samples.csv

@@ -0,0 +1,16 @@
+A,B,C,D
+8.109188439895592,9.33184689521894,9.354787823122058,12.672612419124242
+10.131749781263766,9.33184689521894,9.455474658800501,7.66146433397944
+7.178065881431648,14.342995181076896,9.577728760474645,7.66146410459298
+7.070698283373329,6.826272752289961,9.580692407448097,7.66146410459298
+14.530513949101707,11.837421038147918,8.976055745893488,7.66146410459298
+12.837160139759924,9.33184689521894,13.280120639175362,12.672612419124242
+8.98967523846707,9.33184689521894,5.284223374586355,7.66146410459298
+9.548347716611921,14.342995181076896,9.580597428100837,12.672612419124242
+10.98994063849879,9.33184689521894,9.547969576803277,7.66146410459298
+12.402350479094743,6.826272752289961,9.435510391485826,7.66146410459298
+11.694550072150143,6.826272752289961,9.277034488877351,12.672612419124242
+4.8799780463809785,9.33184689521894,9.389691597155812,12.672612419124242
+9.528364669906528,9.33184689521894,9.586309213728654,12.672612419124242
+9.392042031837274,9.33184689521894,17.540147276068026,7.66146410459298
+12.717374632226587,14.342995181076896,10.13365661827971,12.672612419124242

nbs/blog/posts/robust-beautiful/robust-beautiful.ipynb

@@ -69,7 +69,7 @@
     "In the above figure, four different samples with wildly different\n",
     "distributions--as seen in the swarmplot on the left panel--look exactly\n",
     "the same when visualized with a barplot on the right panel. (You can\n",
-    "download the [dataset](_static/four_samples.csv) to see for yourself.)\n",
+    "download the [dataset](four_samples.csv) to see for yourself.)\n",
     "\n",
     "We're not the first ones (see these articles:\n",
     "[article 1](https://www.nature.com/articles/nmeth.2837),\n",

nbs/read_me.ipynb

@@ -88,13 +88,14 @@
     "You can install this package via `pip`.\n",
     "\n",
     "To install, at the command line run\n",
-    "<!-- ```shell\n",
+    "\n",
+    "```shell\n",
     "conda config --add channels conda-forge\n",
     "conda install dabest\n",
     "```\n",
     "or -->\n",
     "```shell\n",
-    "pip install --upgrade dabest\n",
+    "pip install dabest\n",
     "```\n",
     "You can also [clone](https://help.github.com/articles/cloning-a-repository) this repo locally.\n",
     "\n",
@@ -161,9 +162,9 @@
    "source": [
     "## Contributing\n",
     "\n",
-    "All contributions are welcome; please read the [Guidelines for contributing](https://github.com/ACCLAB/DABEST-python/blob/master/CONTRIBUTING.md) first.\n",
+    "All contributions are welcome; please read the [Guidelines for contributing](CONTRIBUTING.md) first.\n",
     "\n",
-    "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.\n"
+    "We also have a [Code of Conduct](CODE_OF_CONDUCT.md) to foster an inclusive and productive space.\n"
    ]
   },
   {
@@ -172,7 +173,7 @@
    "metadata": {},
    "source": [
     "### A wish list for new features\n",
-    "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**"
+    "If you have any specific comments and ideas for new features that you would like to share with us, please fill this [form](https://docs.google.com/forms/d/1XnF-dkPFUYDPxH9WNXK0L2uU0uv2ZDy4paiCJuk_Kn0)."
    ]
   },
   {
@@ -187,15 +188,25 @@
     "\n",
     "## Testing\n",
     "\n",
-    "To test DABEST, you need to install [pytest](https://docs.pytest.org/en/latest).\n",
+    "To test DABEST, you need to install [pytest](https://docs.pytest.org/en/latest) and [nbdev](https://nbdev.fast.ai/).\n",
     "\n",
-    "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.\n",
+    "- Run `pytest` in the root directory of the source distribution. This runs the test suite in the folder `dabest/tests/mpl_image_tests`. \n",
+    "- Run `nbdev_test` in the root directory of the source distribution. This runs the value assertion tests in parent folder `dabest/tests`\n",
     "\n",
+    "The test suite ensures that the bootstrapping functions and the plotting functions perform as expected.\n",
+    "\n",
+    "For detailed information, please refer to the [test folder](nbs/tests/README.md)\n",
     "\n",
     "## DABEST in other languages\n",
     "\n",
     "DABEST is also available in R ([dabestr](https://github.com/ACCLAB/dabestr)) and Matlab ([DABEST-Matlab](https://github.com/ACCLAB/DABEST-Matlab)).\n"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7106313a",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {