Iakov Davydov

Hi, I've discovered an obscure issue. `birth_death_tree` results are changing if `numpy.save` was used in the code. You need two mostly identical files `1.py` and `2.py`: ```python # 1.py import...

In the documentation, `extract_tree_with_taxa` and `extract_tree_with_taxa_labels` have parameters `is_apply_filter_to_leaf_nodes` and `is_apply_filter_to_internal_nodes`. In reality there are no such parameters, if you are trying to call: ``` subtree = t.extract_tree_with_taxa_labels([...], is_apply_filter_to_leaf_nodes=True) ```...

error occurs in the inner function, but only reported in the outer function

1

When calling nested functions, the error is reported in the outer function `outer_f()`, while it happens in the inner function `inner_f()`. In complex cases this is very difficult to debug....

distributed learning for Tabular (parallelization beyond a single node)

5

Hi, Looking at the source code, it seems to me that parallelization beyond a single node is currently not supported for Tabular by autogluon. I didn't find an issue dedicated...

no way to choose screen with hs.canvas.new

1

Hi, I would like to show canvas on the mainScreen (`hs.screen.mainScreen`). Unfortunately, canvas is always created on the same screen (I'd guess primary screen). Here's the code I'm using: ```lua...

reading gctx from a non-fs file object

1

Hi, In our settings there is often a need to read a `.gctx` file from a non-file (i.e. python file object). Currently it is not possible with cmapPy. The parse...

### Summary `DESCRIPTION` file has the following line: ``` Remotes: GuangchuangYu/treeio ``` This line forces tools like renv (or pak, I think) to gather the latest treeio from github.com, instead...

R terminal doesn't execute `~/.Rprofile` if renv is enabled and `RENV_CONFIG_USER_PROFILE=TRUE` is set in `~/.Renviron`

5

**Describe the bug** R doesn't execute `~/.Rprofile` if renv is enabled and `RENV_CONFIG_USER_PROFILE=TRUE` is set in `~/.Renviron`. Background: renv is not supposed to source `~/.Rprofile` by default, but this can...

an error becomes a message when calling hm1 + hm2 from draw

1

Normally, when adding two heatmaps with different number of rows, an error is generated. However in this code, a message is outputted instead of an error: ``` r m1 heatmap...

easy to accidentally overwrite a repository when calling `repo_add()`

1

As far as I understand, the following code: `pak::repo_add("foo")` is equivalent to `pak::repo_add(EXTRA='foo')`. This could lead to an unexpected behavior when having something like this: ``` echo "pak::repo_add('foo1')" >> ~/.Rprofile...