Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix how we structure the run notebook rules. #1384

Merged
merged 1 commit into from
Jun 3, 2019
+26 −20
Merged

Fix how we structure the run notebook rules. #1384

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 12 additions & 12 deletions .travis.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,40 +29,40 @@ jobs:
script: make docker
- name: smFISH Notebook
if: type = push and branch =~ /^(master|merge)/
script: travis_wait make install-dev run__notebooks/py/smFISH.py
script: travis_wait make install-dev notebooks/py/smFISH.py
- name: MERFISH Notebook
if: type = push and branch =~ /^(master|merge)/
script: travis_wait make install-dev run__notebooks/py/MERFISH.py
script: travis_wait make install-dev notebooks/py/MERFISH.py
- name: osmFISH Notebook
if: type = push and branch =~ /^(master|merge)/
script: make install-dev run__notebooks/py/osmFISH.py
script: make install-dev notebooks/py/osmFISH.py
- name: DARTFISH Notebook
if: type = push and branch =~ /^(master|merge)/
script: make install-dev run__notebooks/py/DARTFISH.py
script: make install-dev notebooks/py/DARTFISH.py
- name: Simulation Notebook
if: type = push and branch =~ /^(master|merge)/
script: make install-dev run__notebooks/py/Starfish_simulation.py
script: make install-dev notebooks/py/Starfish_simulation.py
- name: ISS Notebook
if: type = push and branch =~ /^(master|merge)/
script: make install-dev run__notebooks/py/ISS.py
script: make install-dev notebooks/py/ISS.py
- name: BaristaSeq Notebook
if: type = push and branch =~ /^(master|merge)/
script: make install-dev run__notebooks/py/BaristaSeq.py
script: make install-dev notebooks/py/BaristaSeq.py
- name: SeqFISH Notebook
if: type = push and branch =~ /^(master|merge)/
script: make install-dev run__notebooks/py/SeqFISH.py
script: make install-dev notebooks/py/SeqFISH.py
# - name: STARmap Notebook
# if: type = push and branch =~ /^(master|merge)/
# script: make install-dev run__notebooks/py/STARmap.py
# script: make install-dev notebooks/py/STARmap.py
- name: 3D smFISH data processing example
if: type = push and branch =~ /^(master|merge)/
script: make install-dev run__3d_smFISH.py
script: make install-dev 3d_smFISH.py
- name: iss_cli.sh data processing example
if: type = push and branch =~ /^(master|merge)/
script: make install-dev run__iss_cli.sh
script: make install-dev iss_cli.sh
- name: iss_pipeline.py data processing example
if: type = push and branch =~ /^(master|merge)/
script: make TESTING=1 install-dev run__iss_pipeline.py
script: make TESTING=1 install-dev iss_pipeline.py
- name: Released Notebooks
if: type = cron and branch =~ /^(master|merge)/
script: make check-notebooks install-released-notebooks-support run-notebooks
Expand Down
8 changes: 4 additions & 4 deletions docs/source/_static/data_processing_examples/subdir.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,15 +1,15 @@
path := docs/source/_static/data_processing_examples
py_files := $(wildcard $(path)/*.py)
sh_files := $(wildcard $(path)/*.sh)
py_run_targets := $(patsubst $(path)/%,run__%,$(py_files))
sh_run_targets := $(patsubst $(path)/%,run__%,$(sh_files))
py_run_targets := $(patsubst $(path)/%,%,$(py_files))
sh_run_targets := $(patsubst $(path)/%,%,$(sh_files))

PYTHON := ipython

run-examples: $(py_run_targets) $(sh_run_targets)

$(py_run_targets): run__% :
$(py_run_targets): % :
[ -e $(path)/$*.skip ] || $(PYTHON) $(path)/$*

$(sh_run_targets): run__% :
$(sh_run_targets): % :
[ -e $(path)/$*.skip ] || $(SHELL) $(path)/$*
14 changes: 10 additions & 4 deletions notebooks/subdir.mk
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
py_files := $(wildcard notebooks/py/*.py)
pypath := notebooks/py
py_files := $(wildcard $(pypath)/*.py)
ipynb_files := $(wildcard notebooks/*.ipynb)
py_run_targets := $(addprefix run__, $(py_files))
py_run_targets := $(patsubst $(pypath)/%,%,$(py_files))
py_check_targets := $(addprefix check__, $(py_files))
ipynb_validate_targets := $(addprefix validate__, $(ipynb_files))
ipynb_regenerate_targets := $(addprefix regenerate__notebooks/, $(addsuffix .ipynb, $(notdir $(basename $(py_files)))))
py_regenerate_targets := $(addprefix regenerate__notebooks/py/, $(addsuffix .py, $(notdir $(basename $(ipynb_files)))))
PYTHON := python
PYTHON := ipython

fast: $(ipynb_validate_targets)
run-notebooks: $(py_run_targets)
Expand All @@ -14,7 +15,10 @@ validate-notebooks: $(ipynb_validate_targets)
regenerate-ipynb: $(ipynb_regenerate_targets)
regenerate-py: $(py_regenerate_targets)

$(py_run_targets): run__%.py :
$(py_run_targets): %.py :
[ -e $*.py.skip ] || $(PYTHON) $(pypath)/$*.py

$(py_files): %.py :
[ -e $*.py.skip ] || $(PYTHON) $*.py

$(py_check_targets): check__%.py :
Expand All @@ -30,3 +34,5 @@ $(ipynb_regenerate_targets): regenerate__notebooks/%.ipynb : notebooks/py/%.py

$(py_regenerate_targets): regenerate__notebooks/py/%.py : notebooks/%.ipynb
nbencdec encode notebooks/$*.ipynb notebooks/py/$*.py

.PHONY : $(py_files)