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add workflow cli #274

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f4e45c0
fix(images): add diff static
cameronraysmith Dec 1, 2023
ca7c24c
fix: add gitkeep to src folder
cameronraysmith Dec 1, 2023
d6bb660
fix(gitignore): update hydra and flyte exclusions
cameronraysmith Dec 1, 2023
c7bb6e5
feat(flyte): add local cluster config file
cameronraysmith Dec 1, 2023
40d2e77
feat(flyte): add config file template
cameronraysmith Dec 1, 2023
06f5c5e
feat(envrc): add direnv activation of dotenv
cameronraysmith Dec 1, 2023
f8a1b5c
feat(make): load dotenv variables
cameronraysmith Dec 1, 2023
18ec4c4
feat(dotenv): add example `.env` file
cameronraysmith Dec 1, 2023
a9d6956
fix(containerfiles): rename folder
cameronraysmith Dec 1, 2023
dcc1dd9
fix(containerfiles): use Dockerfile extension
cameronraysmith Dec 1, 2023
5b34a18
fix(make): add system/dev helpers
cameronraysmith Dec 1, 2023
032e152
feat: add pkg dockerfile
cameronraysmith Dec 1, 2023
2627f94
feat: add gpu dockerfile
cameronraysmith Dec 1, 2023
532bc50
feat(make): add poetry dev commands
cameronraysmith Dec 1, 2023
b71338c
feat(pyproject): switch to poetry build
cameronraysmith Dec 1, 2023
d32e9b5
fix(dnadiffusion): use version from pyproject.toml
cameronraysmith Dec 1, 2023
158e633
feat(dnadiffusion): add dataclass auto-creation
cameronraysmith Dec 1, 2023
39c1627
feat(dnadiffusion): add constants
cameronraysmith Dec 1, 2023
ed818aa
feat(dnadiffusion): configure logging
cameronraysmith Dec 1, 2023
cd3cca4
feat(dnadiffusion): add hydra cli
cameronraysmith Dec 1, 2023
2a7e657
feat(dnadiffusion): add example workflows
cameronraysmith Dec 1, 2023
c176733
feat(argo): add container build workflow
cameronraysmith Dec 1, 2023
2ba00c5
feat(github): add environment setup action
cameronraysmith Dec 1, 2023
904fc8a
feat(CI): add CI workflow
cameronraysmith Dec 1, 2023
a4f05db
chore(poetry): add lockfile
cameronraysmith Dec 1, 2023
94db685
fix(pandas): reenable `>2` via flytekit fork
cameronraysmith Dec 1, 2023
02d8a7e
fix(make): add CI targets
cameronraysmith Dec 1, 2023
445546a
fix(pyproject): add workflows extras
cameronraysmith Dec 2, 2023
519b978
fix(cli): use version from pyproject
cameronraysmith Dec 2, 2023
a769f2c
fix(poetry): update lockfile
cameronraysmith Dec 2, 2023
629f6c2
fix(actions): build `workflow_dispatch` only
cameronraysmith Dec 2, 2023
296234e
fix(actions): docker `workflow_dispatch` only
cameronraysmith Dec 2, 2023
96e38aa
fix(actions): CI only runs tests by default
cameronraysmith Dec 2, 2023
bcdc22d
chore(lint)
cameronraysmith Dec 2, 2023
4a63a87
fix(actions): add build-images
cameronraysmith Dec 2, 2023
ebe6074
fix(CI): rename config job
cameronraysmith Dec 2, 2023
a95f049
fix(execute): set default remote project
cameronraysmith Dec 2, 2023
900ac5b
test(CI): enable workflow debug
cameronraysmith Dec 2, 2023
2e2677b
fix(pyproject): update description
cameronraysmith Dec 2, 2023
bea9a4e
test(CI): enable test debug
cameronraysmith Dec 2, 2023
ce43908
fix(pyproject): add poe task to downgrade on cpu
cameronraysmith Dec 2, 2023
c7976ab
fix(actions): downgrade to torch cpu on setup
cameronraysmith Dec 2, 2023
1f404f5
fix(CI): move test debug step before lint
cameronraysmith Dec 2, 2023
7218a32
fix(CI): also build-images on `execute-workflow`
cameronraysmith Dec 2, 2023
3339950
fix: update runners
cameronraysmith Dec 2, 2023
74fdb80
fix(containers): add workflows extras
cameronraysmith Dec 2, 2023
220eae2
fix(codecov): add explicit config file
cameronraysmith Dec 2, 2023
dd1bd25
chore(github): add security policy
cameronraysmith Dec 2, 2023
cc6b030
fix(build-images): use name part slug as lowercase
cameronraysmith Dec 2, 2023
3bc28aa
fix: rename containerfiles dir to containers
cameronraysmith Dec 2, 2023
66570b4
fix: use containers dir
cameronraysmith Dec 2, 2023
460687e
fix(containers): install git in pkg dockerfile
cameronraysmith Dec 2, 2023
88cdacb
fix(argo): resource requests for gpu image build
cameronraysmith Dec 2, 2023
e433c91
fix: install zlib1g-dev for pybedtools compilation
cameronraysmith Dec 3, 2023
4bac31b
fix(argo): increase disk request for pkg image
cameronraysmith Dec 3, 2023
3ae341b
chore(labels): update
cameronraysmith Dec 3, 2023
72450e9
fix(codecov): set 10% threshold
cameronraysmith Dec 3, 2023
144b1ec
test(CI): disable skip-duplicate-runs
cameronraysmith Dec 3, 2023
7ee8f89
fix(test-release): only on dispatch
cameronraysmith Dec 3, 2023
535ebdf
fix(CD): add workflow
cameronraysmith Dec 3, 2023
36e6252
fix(documentation): workflow dispatch only
cameronraysmith Dec 3, 2023
2742287
fix(docs): update build
cameronraysmith Dec 3, 2023
655906f
fix: rename inactivity
cameronraysmith Dec 3, 2023
a973dc9
fix: move deprecated workflows to folder
cameronraysmith Dec 3, 2023
eab0ea0
fix(make): add workflow execution targets
cameronraysmith Dec 3, 2023
08e968f
fix(env): update example
cameronraysmith Dec 3, 2023
a4b1174
fix(make): update ghcr in `tag_images`
cameronraysmith Dec 3, 2023
81ad618
feat(conda): virtual-packages spec for conda-lock
cameronraysmith Dec 3, 2023
66f01f6
fix(pyproject): configure conda-lock
cameronraysmith Dec 3, 2023
8ab24c6
feat(conda): add conda-lock file
cameronraysmith Dec 3, 2023
5c8d6ec
fix(conda): note deprecation in manual environment
cameronraysmith Dec 3, 2023
3c898e5
fix(containers): use conda-lock env in conda image
cameronraysmith Dec 3, 2023
db66457
fix(argo): add mode parameter
cameronraysmith Dec 3, 2023
ba212aa
fix(CI): remove skip-duplicate-runs
cameronraysmith Dec 3, 2023
4dd3de2
fix(make): add explicit `run_dev` target
cameronraysmith Dec 3, 2023
938c159
fix(build-images): specify mode variable
cameronraysmith Dec 3, 2023
228c31e
fix(labels): add CI workflow configuration
cameronraysmith Dec 3, 2023
9a7e174
fix(CI): configure label-based control flow
cameronraysmith Dec 3, 2023
7148772
fix(CI): print variable values
cameronraysmith Dec 3, 2023
0409c7e
fix(CI): use standard if syntax in set-variables
cameronraysmith Dec 3, 2023
90aba9f
fix: ImportPathMismatchError caused by `./notebooks/dnadiffusion.py`
cameronraysmith Dec 3, 2023
a2a4d53
fix(conftest): catch errors for event loops
cameronraysmith Dec 3, 2023
b2a1c81
fix(pyproject): pin pytest-asyncio `<0.23.0`
cameronraysmith Dec 3, 2023
89fccdf
fix(CI): use `!` negation
cameronraysmith Dec 3, 2023
3000d5b
fix(CI): do not set default action var outputs
cameronraysmith Dec 3, 2023
0d14b44
test(CI): check var outputs
cameronraysmith Dec 3, 2023
38d7678
fix(CI): send vars to GITHUB_OUTPUT not ENV
cameronraysmith Dec 3, 2023
7da8bff
Revert "fix(CI): do not set default action var outputs"
cameronraysmith Dec 3, 2023
70b2f55
fix(CI): name action variable step
cameronraysmith Dec 3, 2023
93bae65
fix(CI): string quote negation
cameronraysmith Dec 3, 2023
487c52b
fix(CI): use string comparison
cameronraysmith Dec 3, 2023
bc04f79
fix(CI): limit docs build to ready for review
cameronraysmith Dec 3, 2023
50001de
fix(build-images): accept string input on call
cameronraysmith Dec 3, 2023
24181a5
fix(build-images): set mode env var
cameronraysmith Dec 3, 2023
e90718c
fix(build-images): use `inputs` context directly
cameronraysmith Dec 3, 2023
a04984f
fix(hydra): branch name `GITHUB_HEAD_REF` on PRs
cameronraysmith Dec 4, 2023
9035537
Revert "fix(hydra): branch name `GITHUB_HEAD_REF` on PRs"
cameronraysmith Dec 4, 2023
b066ad6
fix(hydra): add clause for detached head state
cameronraysmith Dec 4, 2023
35f602d
feat(pyproject): add plumbum to workflows deps
cameronraysmith Dec 4, 2023
123d01f
fix(hydra): docstring git_info_to_workflow_version
cameronraysmith Dec 4, 2023
0cc9b7c
fix(hydra): use plubmum instead of subprocess
cameronraysmith Dec 4, 2023
0fff5c4
fix(CI): generate flyte config file before tests
cameronraysmith Dec 4, 2023
d9f88af
fix(CI): decouple tests from image build
cameronraysmith Dec 4, 2023
2e08d25
feat(make): add target to test detached head
cameronraysmith Dec 4, 2023
bcc432a
fix(pyproject): comment hypothetical linux-aarch64
cameronraysmith Dec 4, 2023
c5e6ce3
chore(containers): add deprecated conda manual
cameronraysmith Dec 4, 2023
a9f6d22
fix(conda-lock): update cuda `12.3.0`
cameronraysmith Dec 4, 2023
22aad49
feat(containers): add micromamba image
cameronraysmith Dec 4, 2023
cc676ae
feat(argo): build conda container image
cameronraysmith Dec 4, 2023
3b02e1a
fix(build-image): build conda image
cameronraysmith Dec 4, 2023
1370bbf
fix(containers): update micromamba to user-based
cameronraysmith Dec 4, 2023
3b79a19
fix(containers): use conda-lock cli to install env
cameronraysmith Dec 4, 2023
82ef993
fix(containers): remove redundant ENV LANG
cameronraysmith Dec 4, 2023
cf31f23
fix(containers): use full path to condax
cameronraysmith Dec 4, 2023
1cabf8f
fix(container): use full path to conda-lock
cameronraysmith Dec 4, 2023
439fa3b
fix(pyproject): add pip to conda-lock pkgs
cameronraysmith Dec 4, 2023
340deda
fix(pyproject): conda-lock outputs env and lock
cameronraysmith Dec 4, 2023
52ab090
fix(conda-lock): add pip
cameronraysmith Dec 4, 2023
a974ee6
fix(containers): use ensure-path for condax
cameronraysmith Dec 4, 2023
a30cd7e
fix(containers): manually set path for local bin
cameronraysmith Dec 4, 2023
c67e817
fix(actions): use `inputs` context
cameronraysmith Dec 4, 2023
8250b56
fix(containers): manually construct home variable
cameronraysmith Dec 4, 2023
6ccfbc0
fix(conda-lock): pin to correct fork branch
cameronraysmith Dec 4, 2023
5e38c00
fix(build-images): remove set mode step
cameronraysmith Dec 4, 2023
479a5fa
fix(CI): move concurrency groups to jobs
cameronraysmith Dec 5, 2023
b8ba8c7
fix(CI): job prefix for concurrency groups
cameronraysmith Dec 5, 2023
71461a9
fix(make): get pr source branch from merge ref
cameronraysmith Dec 5, 2023
6fd8d82
test(workflows): reenable cache for all tasks
cameronraysmith Dec 5, 2023
ebdded7
fix(make): remove unused `@`s
cameronraysmith Dec 6, 2023
f82328e
fix: label
cameronraysmith Dec 6, 2023
2b07e8b
fix(HTSeq): install from fork
cameronraysmith Dec 6, 2023
08ac473
fix(pyproject): update to poetry `1.7.1`
cameronraysmith Dec 6, 2023
65a09e7
chore: lint with ruff `0.1.7`
cameronraysmith Dec 6, 2023
c045501
fix(pyproject): pin HTSeq post PR
cameronraysmith Dec 7, 2023
10534a9
feat(make): add local image build targets
cameronraysmith Dec 7, 2023
1a8f411
fix(containers): add swig for HTSeq build
cameronraysmith Dec 7, 2023
d805899
fix(pyproject): remove explicit HTSeq from conda
cameronraysmith Dec 7, 2023
67647cf
fix(conda): update lock files
cameronraysmith Dec 7, 2023
244d2fc
chore(format): use ruff
cameronraysmith Dec 7, 2023
4d39662
fix(make): use ruff to format
cameronraysmith Dec 7, 2023
3140b93
fix(gitignore): add hidden nix folders
cameronraysmith Dec 8, 2023
dbb12d6
fix(make): add devshell/nix targets
cameronraysmith Dec 8, 2023
2e2276a
feat(envrc): enable flake
cameronraysmith Dec 8, 2023
187b0f2
feat(flake): init
cameronraysmith Dec 8, 2023
eecfb0e
chore(flake): init lock
cameronraysmith Dec 8, 2023
1835b99
feat(vscode): add devcontainer recs/settings
cameronraysmith Dec 8, 2023
420df6d
feat(devcontainer): add container and config
cameronraysmith Dec 8, 2023
93d81a0
fix(env): add cachix env examples [no ci]
cameronraysmith Dec 8, 2023
6f24a3e
fix(direnv): disable flake devshell activation
cameronraysmith Dec 8, 2023
a8eac2f
bug(conda-lock): issue reporting only
cameronraysmith Dec 8, 2023
50b50a0
fix(conda-lock): manually update conda-lock files
cameronraysmith Dec 8, 2023
39a9903
fix(pyproject.toml): comments regarding conda-lock
cameronraysmith Dec 8, 2023
b32c347
fix(build): disable conda image build
cameronraysmith Dec 8, 2023
0361ce4
fix(vscode): update search and watcher excludes
cameronraysmith Dec 8, 2023
3c3eb5a
fix(vscode): exclude local venv from search/watch
cameronraysmith Dec 8, 2023
3e4cb61
fix(poetry): add local config to use `./.venv`
cameronraysmith Dec 9, 2023
d9c840d
fix(flake): disable devenv poetry config
cameronraysmith Dec 9, 2023
aa03ed6
fix(direnv): reenable flake devshell as default
cameronraysmith Dec 9, 2023
41f1fb2
fix(pyproject): refactor into smaller dep groups
cameronraysmith Dec 10, 2023
8560fca
fix(poetry): update lock
cameronraysmith Dec 10, 2023
cc60a97
feat(flake): build devshell env with poetry2nix
cameronraysmith Dec 10, 2023
fdea6ee
chore(flake): update lock
cameronraysmith Dec 10, 2023
203bbe8
feat(flyte): add config for browser auth
cameronraysmith Dec 10, 2023
7a53e99
chore(env): add variable for flytectl config template
cameronraysmith Dec 10, 2023
a172dff
fix(make): use env vars in `update_config`
cameronraysmith Dec 10, 2023
f3cdcd5
fix(flake): remove default activation of bioinformatics group
cameronraysmith Dec 10, 2023
b8be2ea
chore(flake): update lock
cameronraysmith Dec 10, 2023
65ddb09
fix(flake): add `yq-go` to devshell
cameronraysmith Dec 10, 2023
8e6e8ae
fix(devcontainer): disable direnv extension
cameronraysmith Dec 10, 2023
60a0ca6
fix(devcontainer): forward port `53593`
cameronraysmith Dec 10, 2023
1306194
fix(direnv): disable default `use flake`
cameronraysmith Dec 10, 2023
6041398
fix(poetry): add markers for sys_platform
cameronraysmith Dec 10, 2023
f62ba87
fix(pyproject): reorganize
cameronraysmith Dec 10, 2023
b8d4065
fix(setup_environment): use dep groups instead of extras
cameronraysmith Dec 10, 2023
5181346
feat(make): add codespace targets
cameronraysmith Dec 10, 2023
84d00cf
fix(flake): poetry2nix flake-utils follows flake
cameronraysmith Dec 10, 2023
e17d2f6
feat(vscode): add debug launch configuration
cameronraysmith Dec 10, 2023
6fed0fd
fix: downgrade mysql-connector-python to version with setup.py
cameronraysmith Dec 12, 2023
7dbdcf3
fix: disable mysql connector
cameronraysmith Dec 12, 2023
e1013b0
feat(make): update codespace code targets
cameronraysmith Dec 12, 2023
3856416
fix(devcontainer): move cloudcode to recs
cameronraysmith Dec 12, 2023
771b710
fix(flake): add buildInputs
cameronraysmith Dec 12, 2023
1d895ba
fix(pyproject): reorganize
cameronraysmith Dec 12, 2023
4a78dff
chore(gitignore): add manual direnv folder
cameronraysmith Dec 12, 2023
8089904
feat(flake): add script to activate flake like direnv `use flake`
cameronraysmith Dec 12, 2023
8c9d51b
feat(make): add target to call flake devshell script
cameronraysmith Dec 12, 2023
5ac91fa
fix(make): declare devshell PHONY
cameronraysmith Dec 12, 2023
a5b7308
fix(devshell): add helper script
cameronraysmith Dec 12, 2023
ae841fc
fix(docs): point to make in dev section
cameronraysmith Dec 12, 2023
2195be5
feat(make): export requirements.txt with poetry
cameronraysmith Dec 13, 2023
2853d96
fix(pyproject): additional conda-lock reqs from pypi
cameronraysmith Dec 13, 2023
b00c136
chore(conda-lock): not functional
cameronraysmith Dec 13, 2023
13272da
feat(requirements): add poetry exported pip requirements
cameronraysmith Dec 13, 2023
0a57a9f
fix(pkg.Dockerfile): separate dependency installation from package
cameronraysmith Dec 13, 2023
0dafac8
fix(gpu.Dockerfile): separate dependency installation from package
cameronraysmith Dec 13, 2023
c4be807
test(lrwine): toggle parameters to trigger rebuild
cameronraysmith Dec 13, 2023
db4f299
fix(pyproject): adopt htseq `2.0.5`
cameronraysmith Dec 15, 2023
66d663b
chore(poetry): update lock
cameronraysmith Dec 15, 2023
e0713c3
chore(conda): update lock
cameronraysmith Dec 15, 2023
a32159d
fix(devcontainer): remove make extension
cameronraysmith Dec 15, 2023
abee230
fix(flake): reenable bioinformatics group
cameronraysmith Dec 15, 2023
2069869
fix(pyproject): uniform dep naming
cameronraysmith Dec 15, 2023
dc0c742
fix(requirements): update pip requirements
cameronraysmith Dec 15, 2023
dc636fe
fix(vscode): update theme
cameronraysmith Jul 30, 2024
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fix(pyproject): pin HTSeq post PR
htseq/htseq#74
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
  • Loading branch information
cameronraysmith committed Dec 7, 2023
commit c0455010f16e1f88931dedc59bbbf9b8aa1e2a20
8 changes: 4 additions & 4 deletions poetry.lock

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions pyproject.toml
Original file line number Diff line number Diff line change
@@ -102,7 +102,7 @@ click = "8.1.7"
einops = "0.7.0"
genomepy = "0.16.1"
gimmemotifs = "0.18.0"
HTSeq = { git = "https://github.com/cameronraysmith/htseq.git", branch = "setup-sin-numpy" }
HTSeq = { git = "https://github.com/htseq/htseq.git", rev="d312d39187362c8c9664fa8d127ee0fb24733152" }
# 1.3.0 never released to bioconda
gtfparse = {version = "1.3.0", source = "pypi"}
jupyterlab = "4.0.9"
@@ -294,7 +294,7 @@ virtual_package_spec = "environments/conda/virtual-packages.yml"
[tool.conda-lock.dependencies]
# transient fork dependency to allow pandas >=2
flytekit = { git = "https://github.com/cameronraysmith/flytekit.git", branch = "3928-pandas-2"}
HTSeq = { git = "https://github.com/cameronraysmith/htseq.git", branch = "setup-sin-numpy" }
HTSeq = { git = "https://github.com/htseq/htseq.git", rev="d312d39187362c8c9664fa8d127ee0fb24733152" }
# not available in conda channels
hydra-zen = {source = "pypi"}
hydra-joblib-launcher = {source = "pypi"}