Add plots subpackage
#67
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This is a complete restructuring of the `epi.plots` module from previous
releases. This commit creates a subpackage `epi.plots`
to handle plotting operations from various models. This subpackage
currently has one other module `web` which handles web-based plotting
via `plotly`, a new experimental dependency.
Changelist:
- Add new requirement `plotly` to `README-nightly.py`
- Add subpackage `epi.plots` to `__init__.py`
- Create subpackage `epi.plots` (and remove old module)
- Add `web` module to `epi.plots` subpackage
- Update testing suite
- Replace `test_transforms.py` with `test_plotting.py` for
`epi.plots` subpackage
Additional Notes:
Deprecation Warning (severe):
This commit deprecates the entire `epi.plots` module.
Release Notes (major):
Due to this severe deprecation and the obvious restructuring of
internal code, these features will likely be released early in the
alpha stage of epispot v3 via `epispot-nightly`.
This commit greatly simplifies the requirements in the epispot project: - `requirements.txt`: Basic requirements needed to run the stable version - `requirements-nightly.txt`: Basic requirements plus experimental dependencies for the nightly version of epispot - `requirements-dev.txt`: All requirements for the nightly version plus helpful packages used in the development process We have also kept `bin/requirements.txt` separately, but all these requirements are specified in the nightly requirements file as well. Changelist: - Update Travis CI to use dev requirements - Add new requirement specifications to the nightly README - Create new requirements files - Update `setup-nightly.py` to include experimental dependencies Additional Notes: Fixes (major): This commit fixes the failing Travis CI build from `df13d29b9b7e0b92654576f1f76a2a0d88418083`.
This commit is intended to fix an error in the Travis CI workflow due to incorrect dependency specifications in `plotly`. Plotly requires `pandas` to run but `pandas` is not explicitly defined as a dependency so it is not installed by `pip` automatically. Because of this, it is listed as a separate dependency to `epispot`. Changelist: - Add `pandas` to `requirements-nightly.txt` - Add `pandas` to `requirements-dev.txt` Additional Notes: Fixes (major): Fix `02202b802793a00c4cb41d8f060d5fb23fb40622`
This commit updates the `plotly` graph styling used in `epi.plots.web.model()` to use: - Times New Roman by default, followed by a serif font - Larger font size (`24px`) - Greater margins (`250px` left and right, `150px` top and bottom) Changelist: - Update graphing styles in `epi.plots.web`
Stacked area charts are now available for compartmental models in `epi.plots.web`, implemented via the function `stacked`. This function takes all the same arguments as the `model` function and uses all the same themes; only the chart type is different. Changelist: - Add stacked area charts to `epi.plots.web` - Add corresponding tests in `tests/test_plotting.py`
The structure label for `epi.plots.web` did not include the `stacked()` function. Additionally, it did not properly include the `()` to indicate that both `model()` and `stacked()` are functions. Changelist: - Fix `## Structure` label on `epi.plots.web`
This commit adds a `title` parameter to all plotting functions. Additionally, the `test_plotting` structure label has been changed to account for the new tests. Changelist: - Add `title` parameter to plots in `epi.plots.web` - Add testing for `title` in `tests/test_plotting.py` - Update structure label in `tests/test_plotting.py`
This commit introduces native plotting via `matplotlib` and `SciencePlots` (for styling purposes). Previously, plots were generated from the `epi.plots.web` module which created in-browser plots rather than native ones. These new native plots can be accessed via `epi.plots.native` and are displayed in a new window. Changelist: - Add `epi.plots.native` module - Add `SciencePlots` to `requirements-nightly.txt` - Add `SciencePlots` to `requirements-dev.txt` - Add dependency check for `SciencePlots` in `epi.plots.__init__.py` and add `native` module - Add `native` plots to tests Additional Notes: Migration (from v2.1.1): The new `epi.plots.native` module will serve as the replacement for the `epi.plots` module in v2.1.1.
* Debug Travis CI * Further debug Travis CI * Update `requirements-dev.txt` * Optimize imports Co-authored-by: q9i <46249765+quantum9Innovation@users.noreply.github.com>
This commit fixes the code coverage lapses identified in "Code Coverage Gaps on `massive-plots` Branch" (#65) by: (1) adding `# pragma: no cover` annotations to `ImportError` (2) adding a `test_full_native` test to test other parameters in `epi.plots.native.model()` Additionally, this commit fixes an identified bug as a result of the increased testing on the `epi.plots.native` module. The `compartments` and `names` parameters to `epi.plots.native.model()` can now be used without errors. Changelist: - Add `# pragma: no cover` annotations to `epi.plots` - Fix bug in `epi.plots.native.model()` - Add a full native test in `tests/plotting` Additional Notes: Issues (minor): - Fixes "Code Coverage Gaps on `massive-plots` Branch #65" - Fixes additional bug discovered in `epi.plots.native.model()`
…to massive-plots
This commit introduces similar stacked area charts to `epi.plots.web.stacked()` in `epi.plots.native`, this adding native support for stacked area charts. Changelist: - Add `epi.plots.native.stacked()` - Add testing support for ^ in `tests/plotting` Additional Notes: Warnings (minor): Occasionally, legend visibility is poor due to the fact that `matplotlib` does not enforce any white background on the legend. A patch will likely fix this.
Parameter values that were stretched across multiple lines have now been concatenated onto one line. Changelist: - Format `tests/plotting`
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Codecov Report
@@ Coverage Diff @@
## master #67 +/- ##
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+ Coverage 87.86% 90.15% +2.29%
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Files 7 9 +2
Lines 412 508 +96
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+ Hits 362 458 +96
Misses 50 50
Continue to review full report at Codecov.
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- Add to `test/x::integrity`
Fix DeepSource error: Re-defined variable from outer scope PYL-W0621 Changelist: - Remove error from epi.plots
Fix DeepSource error: Missing module/function docstring
PY-D0003
Changelist:
- Add docstrings to tests/plotting::
- test_plain_native
- test_full_native
- test_plain_native_stack
- test_full_native_stack
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This pull request introduces 3 alerts when merging f1896c6 into d9dbf03 - view on LGTM.com new alerts:
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Operation massive-plots will be completed after these issues are fixed. |
This commit fixes "Decreased legend visibility on `massive-plots`" (#66) via a suggestion by @lisphilar. Changelist: - Fix `epi.plots.native::stacked` Co-authored-by: Lisphilar <7270139+lisphilar@users.noreply.github.com>
This commit adds a LaTeX installation to the Travis CI install script. LaTeX is needed for the `SciencePlots` package, which uses it in epispot's tests. This also (hopefully) fixes the error from the previous commit on Travis CI. Changelist: - Add LaTeX requirements to `.travis.yml::install` Additional Notes: Fixes (major): Fix `0ca85d13b579e624ca5dfff701a7a7c4c62a0d6c`
This commit fixes the issues described in "Improper handling of `compartments` parameter in `massive-plots`" (#68), which also reappear in 2 'unused variable' alerts on LGTM for PR #67. These can be seen at https://lgtm.com/projects/g/epispot/epispot/rev/pr-4a4c33bcfb0a25433ea10477d7c49b516a6f75d6. Additionally, this commit removes all `compartment` parameters where they are not necessary because similar functionality is already provided by the graphics engine. Changelist: - Remove `compartments` from and restructure `epi.plots.native.model()` - Remove all `compartments` from functions in `epi.plots.web` - Edit `tests/plotting::*full*` to run tests without `compartments` specifications Additional Notes: Fixes (major): Fix "Improper handling of `compartments` parameter in `massive-plots`" (#68) Fix 2 LGTM 'unused variable` alerts in `epi.plots.web` for PR #67
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This pull request introduces 1 alert when merging 3eef7c5 into d9dbf03 - view on LGTM.com new alerts:
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This commit fixes the 'unused import alert' in LGTM for PR #67. This alert can be seen at: https://lgtm.com/projects/g/epispot/epispot/rev/pr-4fc894482dc65aa247dbd5ef531e8bbd3fd15a7c Changelist: - Remove unused import from `epi.plots.native` Additional Notes: Fixes (minor): Fix LGTM 'unused import' alert in `epi.plots.native` for PR #67
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Development v2: massive-plots
New Feature
The massive-plots operation will add a
plotssubpackage toepispot, enabling an even wider array of plots and charts to be generated automatically from epispotModelobjects. As of right now, these includeplotly)matplotlib+SciencePlotsfor styling and optionallyLaTeX)Another operation, mini-plots, will add comparative features to this list and allow charting parameter values and comparing different models. The testing suite for this new module can be found at
tests/plotting. Below are a few screenshots from tests to demonstrate the new charts:Plotly web chart (standard line graph of the SEIR model)
Plotly web chart (stacked area graph of the SEIR model)
Matplotlib native chart (standard line graph of the SEIR model: no LaTeX)
Matplotlib native chart (stacked area graph of the SEIR model: with LaTeX)
Known Issues
There is one noted issue about native stacked area plots, which you can see in #66.
This problem will not affect any other part of epispot's codebase.
Code Breakdown
Additional Notes
Deprecation Warning (severe):
This commit deprecates the entire
epi.plotsmodule.Release Notes (major):
Due to this severe deprecation and the obvious restructuring of
internal code, these features will likely be released early in the
alpha stage of epispot v3 via
epispot-nightly.Migration (from v2.1.1):
The new
epi.plots.nativemodule will serve as the replacement for theepi.plotsmodule in v2.1.1.Warnings (minor):
Occasionally, legend visibility is poor due to the fact that
matplotlibdoes not enforce any white background on the legend.A patch will likely fix this. See #66 for more information.