From f663f5f8368c3c42cab5ffb017c80f3ebae73dd8 Mon Sep 17 00:00:00 2001 From: Serge Koudoro Date: Mon, 29 Jul 2019 18:00:57 -0400 Subject: [PATCH 1/8] rename author link to community --- docs/source/{authors_link.rst => community.rst} | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) rename docs/source/{authors_link.rst => community.rst} (95%) diff --git a/docs/source/authors_link.rst b/docs/source/community.rst similarity index 95% rename from docs/source/authors_link.rst rename to docs/source/community.rst index ec332c930..347d6cf72 100644 --- a/docs/source/authors_link.rst +++ b/docs/source/community.rst @@ -1,6 +1,16 @@ -======== -Credits -======== +========= +Community +========= + +Join Us! +-------- + +- via Slack +- via mailing list +- via github + +Contributors +------------ .. raw:: html From 720f35bca504182fdbce3370e7739a00b2945207 Mon Sep 17 00:00:00 2001 From: Serge Koudoro Date: Mon, 29 Jul 2019 18:01:10 -0400 Subject: [PATCH 2/8] update index --- docs/source/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index 6280a2096..9f0c07954 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -13,5 +13,5 @@ test reference/index contributing_link release-history - authors_link + community From 54f435ad2cb8ed69c20ba0d8ad1b679047e1a3d2 Mon Sep 17 00:00:00 2001 From: Serge Koudoro Date: Mon, 29 Jul 2019 18:01:26 -0400 Subject: [PATCH 3/8] add installation instructions --- docs/source/_templates/page.html | 2 +- docs/source/installation.rst | 74 +++++++++++++++++++++++++++++++- 2 files changed, 74 insertions(+), 2 deletions(-) diff --git a/docs/source/_templates/page.html b/docs/source/_templates/page.html index 1b8ba5e25..54f3e5b73 100644 --- a/docs/source/_templates/page.html +++ b/docs/source/_templates/page.html @@ -73,7 +73,7 @@

API Tutorial Examples - Community + Community diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 24a17ce01..84cc2ac72 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -2,6 +2,78 @@ Installation ============ -At the command line:: +FURY supports Python 3.5+. You can currently still use Python 2.7 but it will be removed as the Python 2.7 end of life +is on December 2019, 31rst + +Dependencies +------------ + +The mandatory dependencies are: + +- numpy >= 1.7.1 +- vtk >= 8.1.0 +- scipy >= 0.9 + +The optional dependencies are: + +- matplotlib >= 2.0.0 +- dipy >= 0.16.0 + + +Installation with PyPi +---------------------- + +Just use the `pip` command line:: $ pip install fury + +Installation with Conda +----------------------- + +Our conda package is on the Conda-Forge channel. You will need to run the following command:: + + $ conda install -c conda-forge fury + +Installation via Source +----------------------- + +**Step 1.** Get the latest source by cloning this repo:: + + $ git clone https://github.com/fury-gl/fury.git + +**Step 2.** Install requirements:: + + $ pip install -r requirements/default.txt + +**Step 3.** Install fury via:: + + $ pip install . + +or:: + + $ pip install -e . + +**Step 4:** Enjoy! + +Test the Installation +--------------------- + +You can check your installation via this command:: + + $ python -c "from fury import get_info; print(get_info())" + +It should return all the informations about FURY. After this success, we recommend you to play with all tutorial! + +Running the Tests +----------------- + +There is two ways to run FURY tests: + +- From python interpreter:: + + $ from fury.tests import test + $ test() + +- From the command line. You need to be on FURY package folder:: + + pytest -svv fury \ No newline at end of file From a5cfb984dfe7ef36daca62fa03725088149fcd08 Mon Sep 17 00:00:00 2001 From: Serge Koudoro Date: Tue, 30 Jul 2019 13:04:04 -0400 Subject: [PATCH 4/8] address @garyfallidis comment --- docs/source/installation.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 84cc2ac72..afd74d555 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -3,7 +3,7 @@ Installation ============ FURY supports Python 3.5+. You can currently still use Python 2.7 but it will be removed as the Python 2.7 end of life -is on December 2019, 31rst +is on December 2019, 31 Dependencies ------------ @@ -62,18 +62,18 @@ You can check your installation via this command:: $ python -c "from fury import get_info; print(get_info())" -It should return all the informations about FURY. After this success, we recommend you to play with all tutorial! +This command will give you all informations about FURY. The next step will be to run a :doc:`Tutorial `. Running the Tests ----------------- -There is two ways to run FURY tests: +There are two ways to run FURY tests: - From python interpreter:: $ from fury.tests import test $ test() -- From the command line. You need to be on FURY package folder:: +- From the command line. You need to be on the FURY package folder:: pytest -svv fury \ No newline at end of file From 64ddceb4c07237a267ec1ab5788fd83d30dc405e Mon Sep 17 00:00:00 2001 From: Serge Koudoro Date: Wed, 31 Jul 2019 19:44:44 -0400 Subject: [PATCH 5/8] address elef comment --- docs/source/installation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/installation.rst b/docs/source/installation.rst index afd74d555..de809dbbf 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -3,7 +3,7 @@ Installation ============ FURY supports Python 3.5+. You can currently still use Python 2.7 but it will be removed as the Python 2.7 end of life -is on December 2019, 31 +is on December 31st 2019. Dependencies ------------ @@ -62,7 +62,7 @@ You can check your installation via this command:: $ python -c "from fury import get_info; print(get_info())" -This command will give you all informations about FURY. The next step will be to run a :doc:`Tutorial `. +This command will give you important information about FURY's installation. The next step will be to run a :doc:`Tutorial `. Running the Tests ----------------- From 6bcec393f45c88cd5254839e055fec5fe7e4cdef Mon Sep 17 00:00:00 2001 From: Serge Koudoro Date: Wed, 31 Jul 2019 22:44:52 -0400 Subject: [PATCH 6/8] Update docs/source/installation.rst Co-Authored-By: Ariel Rokem --- docs/source/installation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/installation.rst b/docs/source/installation.rst index de809dbbf..0dd7a98f5 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -23,7 +23,7 @@ The optional dependencies are: Installation with PyPi ---------------------- -Just use the `pip` command line:: +In a terminal, issue the following command:: $ pip install fury @@ -76,4 +76,4 @@ There are two ways to run FURY tests: - From the command line. You need to be on the FURY package folder:: - pytest -svv fury \ No newline at end of file + pytest -svv fury From cdf01d7560eecb147f0781492e201a6ec7221369 Mon Sep 17 00:00:00 2001 From: Serge Koudoro Date: Thu, 1 Aug 2019 19:42:52 +0200 Subject: [PATCH 7/8] address ariel comment + update some page --- docs/examples/viz_roi_contour.py | 11 ++++++++--- docs/source/community.rst | 6 +++--- docs/source/conf.py | 2 +- docs/source/getting_started.rst | 9 +-------- docs/source/installation.rst | 2 +- 5 files changed, 14 insertions(+), 16 deletions(-) diff --git a/docs/examples/viz_roi_contour.py b/docs/examples/viz_roi_contour.py index fb7f71348..df94e0201 100644 --- a/docs/examples/viz_roi_contour.py +++ b/docs/examples/viz_roi_contour.py @@ -13,9 +13,14 @@ from dipy.reconst.shm import CsaOdfModel from dipy.data import default_sphere from dipy.direction import peaks_from_model -from dipy.tracking.local import ThresholdTissueClassifier +try: + from dipy.tracking.local import ThresholdTissueClassifier as ThresholdStoppingCriterion + from dipy.tracking.local import LocalTracking +except ModuleNotFoundError: + from dipy.tracking.stopping_criterion import ThresholdStoppingCriterion + from dipy.tracking.local_tracking import LocalTracking + from dipy.tracking import utils -from dipy.tracking.local import LocalTracking from dipy.tracking.streamline import Streamlines from fury import actor, window from fury.colormap import line_colors @@ -38,7 +43,7 @@ min_separation_angle=45, mask=white_matter) -classifier = ThresholdTissueClassifier(csa_peaks.gfa, .25) +classifier = ThresholdStoppingCriterion(csa_peaks.gfa, .25) seed_mask = labels == 2 seeds = utils.seeds_from_mask(seed_mask, density=[1, 1, 1], affine=affine) diff --git a/docs/source/community.rst b/docs/source/community.rst index 347d6cf72..01e874f52 100644 --- a/docs/source/community.rst +++ b/docs/source/community.rst @@ -5,9 +5,9 @@ Community Join Us! -------- -- via Slack -- via mailing list -- via github +- via `Slack `_ +- via `mailing list `_ +- via `github `_ Contributors ------------ diff --git a/docs/source/conf.py b/docs/source/conf.py index 494e0a98b..6be7352f7 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -31,7 +31,7 @@ # If your documentation needs a minimal Sphinx version, state it here. # -needs_sphinx = '1.6' +needs_sphinx = '2.1' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst index 1fe303def..5850a10ed 100644 --- a/docs/source/getting_started.rst +++ b/docs/source/getting_started.rst @@ -46,14 +46,7 @@ FURY is distributed under the BSD 3 License Credits -------- -The following people have been involved in the development of FURY: - -* Eleftherios Garyfallidis, Indiana University, IN, USA -* Marc-Alexandre Côté, Microsoft Research, Montreal, QC, CA -* David Reagan, Indiana University, IN, USA -* Ranveer Aggarwal, Microsoft, Hyderabad, Telangana, India -* Serge Koudoro, Indiana University, IN, USA -* Karandeep Singh Juneja, India +Go to :doc:`Community page ` to see who have been involved in the development of FURY: Bug reports and support --------------------------- diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 0dd7a98f5..b408b3042 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -62,7 +62,7 @@ You can check your installation via this command:: $ python -c "from fury import get_info; print(get_info())" -This command will give you important information about FURY's installation. The next step will be to run a :doc:`Tutorial `. +This command will give you important information about FURY's installation. The next step will be to run a :doc:`tutorial `. Running the Tests ----------------- From e764c170d70faab05a07c1f6901c3cdd1aeace71 Mon Sep 17 00:00:00 2001 From: Eleftherios Garyfallidis Date: Thu, 1 Aug 2019 14:45:09 -0400 Subject: [PATCH 8/8] Minor syntax change --- docs/source/installation.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/source/installation.rst b/docs/source/installation.rst index b408b3042..9459bc8a0 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -2,8 +2,7 @@ Installation ============ -FURY supports Python 3.5+. You can currently still use Python 2.7 but it will be removed as the Python 2.7 end of life -is on December 31st 2019. +FURY supports Python 3.5+. You can currently still use Python 2.7 but it will soon stop being supported as the Python 2.7 end of life is on December 31st 2019. Dependencies ------------