From a215eda05fadf0a9f23167156327e81498f2c780 Mon Sep 17 00:00:00 2001 From: Manubot Rootstock Contributors <> Date: Wed, 6 Sep 2017 12:27:23 -0400 Subject: [PATCH 1/2] Squash all manubot rootstock commits From https://github.com/greenelab/manubot-rootstock/tree/b5644db59904b5563a79376e51765adf113a02cb --- SETUP.md | 14 +- build/assets/style.csl | 193 +++---------- build/environment.yml | 2 +- ci/deploy.key.enc | Bin 3248 -> 3248 bytes ci/deploy.key.pub | 2 +- content/99.back-matter.md | 5 +- webpage/github-pandoc.css | 593 +++++++++++++++++++++++++++++++++++++- 7 files changed, 639 insertions(+), 170 deletions(-) diff --git a/SETUP.md b/SETUP.md index 6966c8f..abe84f7 100644 --- a/SETUP.md +++ b/SETUP.md @@ -73,6 +73,7 @@ echo https://github.com/$OWNER/$REPO/settings/keys ``` Manually add `deploy.key.pub` (with write access) to GitHub under the repository's deploy key settings (the URL echoed above). +Give the key a descriptive title, such as "Travis CI Manubot". For the next step, you need the [Travis command line client](https://github.com/travis-ci/travis.rb) installed. This program is a Ruby gem: @@ -103,6 +104,14 @@ TRAVIS_ENCRYPT_ID=`grep \ sed --in-place "s/f2f00aaf6402/$TRAVIS_ENCRYPT_ID/g" deploy.sh ``` +Next, limit [concurrent](https://blog.travis-ci.com/2014-07-18-per-repository-concurrency-setting/) Travis CI jobs to ensure previous builds deploy before subsequent ones begin: + +```sh +travis settings \ + --repo=$OWNER/$REPO \ + maximum_number_of_builds --set 1 +``` + The continuous integration configuration is now complete. Clean up: @@ -123,11 +132,14 @@ Now update `README.md` files to reference the new repository: # Perform substitutions sed --in-place "s/greenelab/$OWNER/g" README.md sed --in-place "s/manubot-rootstock/$REPO/g" README.md + +# Remove deletable content file +git rm content/02.delete-me.md ``` ## Finalize -Run `git status` or `git diff` to check that the following files have unstaged changes: +Run `git status` or `git diff --word-diff` to check that the following files have unstaged changes: + `README.md` + `ci/deploy.key.enc` diff --git a/build/assets/style.csl b/build/assets/style.csl index 466e765..a7dd0d8 100644 --- a/build/assets/style.csl +++ b/build/assets/style.csl @@ -1,142 +1,37 @@ - - diff --git a/build/environment.yml b/build/environment.yml index 2d25db2..4272d31 100644 --- a/build/environment.yml +++ b/build/environment.yml @@ -14,7 +14,7 @@ dependencies: - pip: - errorhandler==2.0.1 - ghp-import==0.5.5 - - git+https://github.com/greenelab/manubot@33e512d21218263423de5f0d127aac4f8635468f + - git+https://github.com/greenelab/manubot@367f0b5c8046e5ce2f1e5a0ef555ec29a4aefd59 - opentimestamps-client==0.5.0 - opentimestamps==0.1.0 - pandoc-eqnos==0.16 diff --git a/ci/deploy.key.enc b/ci/deploy.key.enc index 4f7fdd22462858a1e5ec1a14611c9c3a58052ed7..28adfa66e36e6801295509a555478e06e006332f 100644 GIT binary patch literal 3248 zcmV;h3{UeZ3{&ZWQIZTJ#B*|e@!xeuvz}4LZxFmp1n%glFVr;JGIWoJe2fNPgJt-# zN6e*bq8J@8qPjmgJQv6_8Xd!n?QnJ!q$~*ZMzt7N ze49>`a#19UY0AuIv-j}9<>#^VEr5kFF;9j^zx9^`*Jvo+pM(SU9yh!!u)1 zy17{oU!6wT$S8s5sxZU?;ZY?lZrwO%R9?u-q=RHu=~^FtJN?!{-&dqgNQdOebwMAf z|Ff&XXL3NAR_xIjtXWurbOHd-6@REVl#sFW<4;l_`hdq~*)?E|`$YCuPk2_vKoX|? zD~S~@l;Kwj^_^_i{e%jryX^*LI79SJ)9;$2+&lfKC1pvUftSx|m(MV0^4f|M%zApU zy_stp71}_{RU?&B+OS+eH=c-HiUYvON%%^V01=D{U+LEQlj+NOA_*wWBhSOJp~N&i ztd~in5pKHY2qCt6YLBw4_RQ=HWr33Wq-(0ZPkmeR-3489T}`S(t~V}BdH!;Y*V3ej z(HBH*M0$!nMRB6mrA;lk5ERTA#&3W=U4@%*Rh1Nq0~7c~l3y{uerI-wJ}kWRG(hbKJKNL3 zNwh5%VR?)RJ=)I**@7lXbheA1h!dXj9r3?Ne|Zk~bzv_ezNDU%VpD9)WSknpd-;mW z9ou`DmE#Bz@{jO8qb$7=j|JQ!ea0K`!8Xx*(?qaxi%!o6Qk$~WV|D`RMTKAI6VXqq zuxAxinja@R4u} zn=xL>p|@Hf#ez7F@d@jedz}?hcCpZ$PA2-3-_zNkVnWK_hm#5ai zN&`dCtHiQQD(6ilF#1k!$QON_$_xPJyq-0of(IMbDb}$>M{rlS#y7b&B0C;7WitgB z7PyF2$+2c|c~#wYx5x_W`IKiM?Z7DBNC7;oJIPXmkr?#pdUQSew1_*uaY#`)a6^=7 zjbzAh>ys(s=|*uomEVq<*gA3e*M{I1t|dXuNM6Eq8InTIw%ZL2sQrZlK&bFSlO7K9 zx_rVF8~nLwtHDC5I}K94PUF5aXdQj%YDYb-pCihKj-s;8x8fSgD124^FM8FU)ff(e zbiB|U+IWNBOCl1HSwtRe&iaP5GPhUWq0Wt468oXUZqx+Zpiwq&U+F*QlvJ5FnK@B) z{;+}Sl^P1@2`g5xG{b_fu*(albqQ=C@Ex|jvmVws(BO-6srpDrbr$&}^JNG~$GtOTthcM{C!LxR=77!FPV4Cv`^1jP_YRWi$S`Y9K&ur3n$!F`usFbHuk|Z!pv;2!lcS?f zg;KWb$BXCvM+FoVkEA>J6r}VB1a$RKj@h26TZ_7PPm)l$YOK9jt6nfa zZjRzOd_3`!er?vB&L;K3TAqP|OJ!$P&E=M^<3`vgD5w16P#Dy(XHkNVCBv8~x-bw> zckf`SV8b#vou=Fv?t~)~%5Q7L=ezaOAMr3P4^;V^z?G_|tWKkV!tNKkO0Fw|M{8iq z>h(V#%mnAQ!Zktn~nHGi27R zw)Yt&o&zh{bfcX^XV{g0u8kb8yI%TW-+VsnBj-hAvC_@J_DhrrQX!B{AaATzEeh~g zwNn8DOwrqx`6ySZZY@N1vUa zoW3s%lqK260)uot>qVrs@aYO}{m(v7maDgfomKLGXDJjGx#m?2b%NpgV2)T!{vqBA zW-%bK#S-rA%HBmrCTzJSYUiahb$camOGxzRFx7l=4GU=RA#0MYY#h4ul_w1=^BMJJ zYIL)-=wWshNgQ8(`s}lfNGn7}FwmbCIYWf)ebK|M$Cqabc~Og{{j!YSGzvB8KsQ|IKAn^ zW24wG2RI1`rOSiJ=F*HpYCMPd<2v_7N~jvAi+l20(nc7QRV~L*)D*@7qvUagM1q~= z8s$_=M9R~1JWfou3{gY#n`^NRx@GcGejymnLO#LOo9J(Fpm++a;4(ie>eeqYbnByb zDM>43^V|0eTLPo5w(0F7W`*`?#Pmf0j~)*H#V*fd^%mt95=;w!Yxu8`t(Zme9kWti z2SJ~8iimQ<-m&ONwzK49-pl^;Hm;?MFbwuV>1t3|0uCB<3)q}wYkP-ehZQ039rffP zBh(MVQP#ZP6B~j#j7`|qaafXwmB=>*YS^Rbi}aeV4mVEr_@y-t%ZG58JL)bL6%bcn z&z<;!_;?f`t<1I_>}kLyk`X+Id3otR+4o09*x?DRV8h-af;6u!+G!t2S!a>;mbB){ zThU1BU_EAR6shM0xVcC5PZrE84G^EM1U&8ZxFe$_`iTwk^!;C-AwC){hkt^t37NK@ z*|6jlKt;s?c!@eZI^iTmDo=-!x=+xP;|r#tyH#odJQ(Aw#?~>4_1p4Zz!I&(lNgq_ zcwM%WyxgLpKyWVLe9YghyKgA@!v*4B|8d?QsO0+2;gv<_Wj-x-`Zu#T1w%A{KbW$t zEHFeu=0qc#C3)L@K(QdcU>={ZXY6bGs}T;<-nAfG`H^%PKTI$nchWFA3rc}5FnYs;GJwnTu7G0(G@?n)#nuGh^@vT6dE zJt2=>yS({>zqVgTZj7>}w&uNd2dOAT*=e63daLyi=zDf;A|JFDJ6W^?@k6+ZH?GNh zFF*ryc6S}LV!j{;$j^+XFr!fNEen`~Zih8!AH9?3wU(eQWH&y>R<#?OK80BS{q6?C zQA1U|kBpL$YG;ST%qWJTQ;TQnWDF|(BH6Bx@+GtXxTYx+KqHBS9300by;{1P?3BI^j6bBq3&+xGBD!|VDgOt$|jU4 zicq5JsPFBzX3mZe1K*}Ys~s^XJNU11sdSS)S@gac_IrYY9g*0LzK~nI8T1E(F^>vV zVozN@HudP&&fC;KlIJw}@PjnyROG_UTP=WKzMk&a4-~>OdWzc8Txa^DyYW8>98eqo zEq$}YR5#KV;Z=`Y4@^@82tb2&6=|3Rd>@CV!dI|
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+.highlight .vi { + color: #008080 +} +.highlight .il { + color: #099 +} +.highlight .gc { + color: #999; + background-color: #eaf2f5 +} +.type-csharp .highlight .k, +.type-csharp .highlight .kt { + color: #00F +} +.type-csharp .highlight .nf { + color: #000; + font-weight: normal +} +.type-csharp .highlight .nc { + color: #2b91af +} +.type-csharp .highlight .nn { + color: #000 +} +.type-csharp .highlight .s, +.type-csharp .highlight .sc { + color: #a31515 +} From 71bbb53313be891efbc0339b6aeb230ca85bce83 Mon Sep 17 00:00:00 2001 From: Daniel Himmelstein Date: Wed, 6 Sep 2017 12:52:06 -0400 Subject: [PATCH 2/2] Revert build/assets/style.csl path --- build/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build/build.sh b/build/build.sh index f3e1729..3b24e16 100644 --- a/build/build.sh +++ b/build/build.sh @@ -14,7 +14,7 @@ manubot \ --log-level=INFO # pandoc settings -CSL_PATH=https://github.com/dhimmel/manubot-rootstock/raw/5f01555cd81f67591de271bfb564487c65ca3313/build/assets/style.csl +CSL_PATH=build/assets/style.csl DOCX_PATH=build/assets/pandoc-reference.docx BIBLIOGRAPHY_PATH=output/references.json INPUT_PATH=output/manuscript.md