Taxidtools

Latest version: v3.1.1

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2.4.0

**New features**

* Added a `Taxonomy.copy()` method as a shorthand for `copy.deepcopy(Taxonomy)`
* Added an `inplace` argument to `Taxonomy` methods `filterRanks()` and `prune()`, allowing chose whether to return a modified deepcopy of the instance od modifiy it in place

**Improvements**

* Unit tests now use temporary directories to test IO methods
* The `Taxonomy.filter()` method will now return a `ValueError` when attempting to use `root` rank in the filtering instead of creating new root Nodes

**Pending deprecation**

* `Taxonomy.from_json` will be removed in 3.0.0, it is replaced by `read_json`, a module level constructor.
* `load` will be removed in 3.0.0, it is replaced by `read_json`, a module level constructor.
* `Taxonomy.from_taxdump` will be removed in 3.0.0, it is replaced by `read_taxdump`, a module level constructor.
* `load_ncbi` will be removed in 3.0.0, it is replaced by `read_ncbi`, a better-named module level constructor.

**Bug Fix**

* `Taxonomy.listDescendant` now does filter output based on the ranks parameter
* Repaired `Node.node_info` output to actually use newlines instead of printing '\n'

2.3.1

**Distribution**

* It is now possible to install taxidTools from DockerHub:


docker pull gregdenay/taxidtools


* `conda-forge` release should now auomatically find the last release from Github/Pypi

2.3.0

**New features**

* Attempting to access an invalid Node with the Taxonomy __getitem__ method (`Taxonomy["node_id"]`) now returns a specifc `InvalidNodeError`
* Added the `load_ncbi` function as a shorthand for the constructor `Taxonomy.from_taxdump`.

2.2.020210921

**Bug Fix**

* Fixed broken implementation of `Taxonomy.filterRanks`

**Implementation changes**

* `Node` and `Dummy Node` classes now ihnerit from the new _BaseNode classe. No impact on methods and properties.

2.2.3

**Bug Fix**

* Fixed an error in the listDescendant method that affected the prune and filterRanks methods.

**Performance**

* Node.children attribute is now a set, considerably speeding up file loading.

2.2.2

**Bug Fix**

* Fixed some bugged references to Node class

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