Some tests still fail due to upstream reasons so we skip those.
Note also that we are not using nix's pytestCheckHook due to
pysam detecting how it's loaded which conflicts with how
pytestCheckHook runs tests. In addition, the selection mode used
by disabledTests causes more tests than the failing ones to be
skipped, which is undesired.
See the discussion in https://github.com/NixOS/nixpkgs/pull/100823
Right now, running `nixos-rebuild` gives an obscure error:
```
$ nixos-rebuild switch
building Nix...
building the system configuration...
error: Abandoned by upstream. Consider switching to bottom instead
(use '--show-trace' to show detailed location information)
```
(And `--show-trace` adds no useful information.)
The error message doesn't indicate that `ytop` is what's causing the problem.
By adding `ytop` to the error message, configurations that still reference
`ytop` will be easier to debug and fix.
Foremost, the message was discarding double quotes on one side of the
diff, which was super-confusing to me, as I thought that the format
convertor broke that when in fact only whitespace was changed.
I thought I'd cat the files, but then... switching to `diff -u` seemed
self-sufficient. It felt sufficiently non-controversial to push
directly, but certainly feel free to improve further.
These are fixes for problems I ran into with:
- `bazel test //example:cpp-test`
This needed `build --host_javabase='@local_jdk//:jdk'`
- `bazel query 'deps(//example:cpp-test)'`
This needed the same flags as `build`.
Is it contentious to (partially?) configure the default java toolchain? I don't see it as much different than providing the bazel server's java.
It would continue to be configurable/overridable by overriding the flags.
---
And a random notes from this escapade, but https://github.com/bazelbuild/bazel/blob/master/WORKSPACE#L144-L308 looks a little different from https://github.com/NixOS/nixpkgs/blob/master/pkgs/development/tools/build-managers/bazel/bazel_3/src-deps.json so one of them is probably wrong :)
