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-rw-r--r--README.org2
-rw-r--r--guix.scm84
-rw-r--r--manifest.scm12
3 files changed, 50 insertions, 48 deletions
diff --git a/README.org b/README.org
index 5ec53f0..5e5e0a9 100644
--- a/README.org
+++ b/README.org
@@ -31,7 +31,7 @@ For reproducibility, this project is developed using guix.
To launch a guix shell for development, do
#+BEGIN_SRC shell
- guix shell --container --network --pure --manifest=manifest.scm --share=/some/host/directory=/the/upload/directory
+ guix shell --container --network --development --file=guix.scm --share=/some/host/directory=/the/upload/directory
#+END_SRC
which environment that is isolated from the rest of your system.
diff --git a/guix.scm b/guix.scm
index 0c78fc1..2db6063 100644
--- a/guix.scm
+++ b/guix.scm
@@ -1,4 +1,9 @@
-(use-modules (guix packages)
+(use-modules (git oid)
+ (guix gexp)
+ (git bindings)
+ (git reference)
+ (git repository)
+ (guix packages)
(guix git-download)
(gnu packages check)
(gnu packages databases)
@@ -8,38 +13,47 @@
(gnu packages python-check)
((guix licenses) #:prefix license:))
-(let ((commit "4808ae57ac83ef00e679c94fe6844c72f18735b9")
- (revision "2"))
- (package
- (name "genenetwork-qc")
- (version (git-version "0.0.1" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://git.genenetwork.org/fredmanglis/gnqc_py.git")
- (commit commit)))
- (sha256
- (base32
- "14lbdbkqa5aiwldafirgqsfcydbqqbhz30vrf80afxj9sqxcscd9"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "pytest")))))))
- (inputs
- (list python-mypy
- python-pylint
- python-pytest
- python-hypothesis))
- (propagated-inputs
- (list redis))
- (synopsis "GeneNetwork Quality Control Application")
- (description
- "GeneNetwork qc is a quality control application for the data files that
+(define %source-dir (dirname (current-filename)))
+
+(libgit2-init!)
+(define gnqc-py
+ (let ((commit (oid->string
+ (reference-target
+ (repository-head (repository-open %source-dir)))))
+ (revision "3"))
+ (package
+ (name "genenetwork-qc")
+ (version (git-version "0.0.1" revision commit))
+ (source (local-file %source-dir
+ "gnqc_py-checkout"
+ #:recursive? #t
+ #:select? (git-predicate %source-dir)))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest")))))))
+ (inputs
+ (list python-mypy
+ python-pylint
+ python-pytest
+ python-hypothesis))
+ (propagated-inputs
+ (list redis
+ python-redis
+ python-flask
+ python-jsonpickle
+ python-mysqlclient))
+ (synopsis "GeneNetwork Quality Control Application")
+ (description
+ "GeneNetwork qc is a quality control application for the data files that
eventually are used to add to the data in the GeneNetwork project.")
- (home-page "https://git.genenetwork.org/fredmanglis/gnqc_py")
- (license license:agpl3+)))
+ (home-page "https://git.genenetwork.org/fredmanglis/gnqc_py")
+ (license license:agpl3+))))
+
+(libgit2-shutdown!)
+
+gnqc-py
diff --git a/manifest.scm b/manifest.scm
deleted file mode 100644
index d18be5b..0000000
--- a/manifest.scm
+++ /dev/null
@@ -1,12 +0,0 @@
-(specifications->manifest
- (list "redis"
- "python"
- "python-mypy"
- "python-redis"
- "python-flask"
- "python-magic"
- "python-pylint"
- "python-pytest"
- "python-hypothesis"
- "python-jsonpickle"
- "python-mysqlclient"))