What does "move it into a 'librtd/' subdirectory" mean?

[Benjamin-Lee]

I'm getting the incorrect package structure warning. Its well written, but there is an ambiguous phrase. My directory structure looks like this:

.
├── README.md
├── librtd
│   ├── __init__.py
│   ├── cli.nim
│   ├── cli_wrapper.py
│   └── librtd.nim
├── librtd.nimble
├── setup.py
├── test.fasta
└── tests
    ├── config.nims
    ├── tests.cpython-37m-darwin.so
    └── tests.nim

The entire directory for the project (tests and all) is entitled librtd. Thus, the warning message could mean:

1. Move it into a subdirectory of librtd/librtd like librtd/librtd/cli/cli.nim.
2. Move it into the subdirectory librtd/librtd.
3. Move it into librtd/ (same level as librtd.nimble).

Which is it?

[Benjamin-Lee]

Additionally, I am still receiving the warning even after adding skipFiles = @["cli.nim"] to the .nimble file

[Benjamin-Lee]

For reference, here's the code I'm working on: https://github.com/Lab41/librtd/tree/python

[dom96]

You've deleted the branch so I can't see it now. Hard to say without seeing the .nimble file and the exact message you got. Did you manage to get it fixed?

[genotrance]

@Benjamin-Lee ping

[Benjamin-Lee]

Still having the same issue after a restructuring. Here's the link to the main repo and here's the current structure:

├─ .github
│  └─ workflows
│     ├─ ci.yml
│     └─ release.yml
├─ benchmarks
│  ├─ .gitignore
│  ├─ benchmark.py
│  └─ requirements.txt
├─ librtd-py
│  ├─ librtdpy
│  │  ├─ librtdpy.nim
│  │  └─ librtdpy.nimble
│  ├─ cli.nim
│  ├─ cli_wrapper.py
│  ├─ librtd.py
│  ├─ setup.py
│  └─ test_output.fasta
├─ librtd
│  ├─ tests
│  │  └─ tests.nim
│  ├─ librtd.nim
│  └─ librtd.nimble
├─ .flake8
├─ .gitignore
├─ LICENSE
├─ README.md
└─ test.fasta

Within the librtd subdirectory, when installing I still get this error:

~/D/P/R/l/librtd ❯❯❯ nimble install -y
   Warning: Package 'librtd' has an incorrect structure. It should contain a single directory hierarchy for source files, named 'librtd', but file 'tests.nim' is in a directory named 'tests' instead. This will be an error in the future.
      Hint: If 'tests' contains source files for building 'librtd', rename it to 'librtd'. Otherwise, prevent its installation by adding `skipDirs = @["tests"]` to the .nimble file.
  Verifying dependencies for librtd@0.0.1
      Info: Dependency on progress@>= 1.1.1 already satisfied
  Verifying dependencies for progress@1.1.1
 Installing librtd@0.0.1
    Prompt: librtd@0.0.1 already exists. Overwrite? -> [forced yes]
   Success: librtd installed successfully.

Here's what my .nimble file looks like:

# Package

version       = "0.0.1"
author        = "Benjamin Lee"
description   = "Generalized k-mer return time distribution calculation"
license       = "Apache-2.0"
skipDirs      = @["tests"]
installExt    = @["nim"]


# Dependencies

requires "nim >= 1.0.4"
requires "progress >= 1.1.1"

[dom96]

Hm, this may be a bug. If you remove the installExt = @["nim"] (which is redundant btw) it works. But it should work with it too I think.

[Benjamin-Lee]

There's another strange thing happening. Take a look:

~/D/P/R/l/librtd ❯❯❯ cat librtd.nimble
# Package

version       = "0.0.1"
author        = "Benjamin Lee"
description   = "Generalized k-mer return time distribution calculation"
license       = "Apache-2.0"
skipDirs      = @["tests"]
installExt    = @["nim"]


# Dependencies

requires "nim >= 1.0.4"
requires "progress >= 1.1.1"⏎                                                                                                                  ~/D/P/R/l/librtd ❯❯❯ nimble install -y
   Warning: Package 'librtd' has an incorrect structure. It should contain a single directory hierarchy for source files, named 'librtd', but file 'tests.nim' is in a directory named 'tests' instead. This will be an error in the future.
      Hint: If 'tests' contains source files for building 'librtd', rename it to 'librtd'. Otherwise, prevent its installation by adding `skipDirs = @["tests"]` to the .nimble file.
  Verifying dependencies for librtd@0.0.1
      Info: Dependency on progress@>= 1.1.1 already satisfied
  Verifying dependencies for progress@1.1.1
 Installing librtd@0.0.1
    Prompt: librtd@0.0.1 already exists. Overwrite? -> [forced yes]
   Success: librtd installed successfully.
~/D/P/R/l/librtd ❯❯❯ cat librtd.nimble
# Package

version       = "0.0.1"
author        = "Benjamin Lee"
description   = "Generalized k-mer return time distribution calculation"
license       = "Apache-2.0"
skipDirs      = @["tests"]


# Dependencies

requires "nim >= 1.0.4"
requires "progress >= 1.1.1"⏎                                                                                                                  ~/D/P/R/l/librtd ❯❯❯ nimble install -y
  Verifying dependencies for librtd@0.0.1
      Info: Dependency on progress@>= 1.1.1 already satisfied
  Verifying dependencies for progress@1.1.1
 Installing librtd@0.0.1
    Prompt: librtd@0.0.1 already exists. Overwrite? -> [forced yes]
   Warning: Package 'librtd' has an incorrect structure. It should contain a single directory hierarchy for source files, named 'librtd', but file 'tests.nim' is in a directory named 'tests' instead. This will be an error in the future.
      Hint: If 'tests' contains source files for building 'librtd', rename it to 'librtd'. Otherwise, prevent its installation by adding `skipDirs = @["tests"]` to the .nimble file.
   Success: librtd installed successfully.
~/D/P/R/l/librtd ❯❯❯ nimble install -y
  Verifying dependencies for librtd@0.0.1
      Info: Dependency on progress@>= 1.1.1 already satisfied
  Verifying dependencies for progress@1.1.1
 Installing librtd@0.0.1
    Prompt: librtd@0.0.1 already exists. Overwrite? -> [forced yes]
   Success: librtd installed successfully.

When I reinstall as usual (with installExt) I get the warning. Removing the installExt and then reinstalling still produces the warning but this time at the end. Reinstalling again without installExt removes the warning.

A fresh install (after uninstalling the lib) produces no warning when installExt is removed.

[Benjamin-Lee]

Might it be a good idea to rename this issue to more clearly reflect what the issue is?

[dom96]

A fresh install (after uninstalling the lib) produces no warning when installExt is removed.

That's because you get the warning about the installed library.