diff --git a/CHANGELOG.md b/CHANGELOG.md
index 00db6a52e5d281f4f58fdca7adfc4025c90fa838..fe941d552e76a9e014ba4f7723842d17ad040b4b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
## Unreleased
### Added
+- Added the PolyChord sampler, which can be accessed by using `sampler='pypolychord'` in `run_sampler`
- `emcee` now writes all progress to disk and can resume from a previous run.
### Changed
diff --git a/Pipfile b/Pipfile
index 258de82a4c2b72f9f7ae4017c89054e6d8dd8db6..2b2b4d23524873c3c066e9c06390e2414eb24601 100644
--- a/Pipfile
+++ b/Pipfile
@@ -6,11 +6,12 @@ name = "pypi"
[packages]
future = "*"
corner = "*"
-numpy = ">=1.9"
+numpy = "==1.15.2"
+ligotimegps = "<=1.2.3"
matplotlib = "<3"
scipy = ">=0.16"
-pandas = "*"
-deepdish = "*"
+pandas = "==0.23.0"
+deepdish = "==0.3.6"
mock = "*"
astropy = "<3"
gwpy = "*"
@@ -23,7 +24,6 @@ emcee = "*"
nestle = "*"
ptemcee = "*"
pymc3 = "*"
-pymultinest = "*"
[requires]
diff --git a/Pipfile.lock b/Pipfile.lock
index 7300f095ed679ab40898a18ef20603994527611d..42634199226773a003c7358eae516c6cd9d1b8f8 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
{
"_meta": {
"hash": {
- "sha256": "dec6b7c15df6450bdbd7946533a3cf8c8d554a48e7ca711787eaf5bfcba6c492"
+ "sha256": "7c1f82e7840646851cc40ded7939ef8a712f4d922ab5cbbceab652366c9a48dc"
},
"pipfile-spec": 6,
"requires": {},
@@ -23,26 +23,39 @@
},
"astropy": {
"hashes": [
- "sha256:13cdf1ba17d2ecbafc9fcb20d82d2aa53f0fc116a815d17357f86c0180215ffc",
- "sha256:22051a03bb268a0426a0170366e4680553028c5f9282f335c575a850e7eb85ef",
- "sha256:32fbaf565bebbbc91b64271e1f08870cf23c63a7f852e848df932324dedc8a07",
- "sha256:53979303beb386038ac6dd69c1d08b148d518a915c8c1f9c45179b5f752739fc",
- "sha256:9f354bdde7fd1261b14379553dc3500956ddba56afc80c021f8592138d827a51",
- "sha256:a8015f84c42051342a2a8ee710868e682b9775a3b7948fdc1e87124bcd6e69dc",
- "sha256:b284f9452dc8330a0bec13713a739d5714f01de5c473a31df80f1719fe56956c",
- "sha256:d46f4e578c2e0b69b0ae4958c426ca12cbf7849c5cadba9200aa8866ae107dfe",
- "sha256:d918ce1da85ee8c90f3e1f40be6a6743d33bcd992fe813bfc193dac8fd7a544a"
+ "sha256:010f5450a45a3d510aa46b98008a50bccfb8f5bc1430736faf0bc953e085c93c",
+ "sha256:0988be682b22c85e70b752967613342a7952075074e823fcb58fd516287d221c",
+ "sha256:0c14fcd0ad8ea3388392587a17384b3574ccc5e2f7db9f8c03b1ee7d78a26e4c",
+ "sha256:104b64643fb6ab05cfdf4a2f0f61d7b85f0a7f36a759683dea1ae9c8b5d957f1",
+ "sha256:1a2a9731cfa7e70104effa507934c0ff61463daf9cf34085ad63ee8f4af1d46e",
+ "sha256:424be12ee173267d8d0a209bd292336dda87f463fb201ec76a974eb25101016b",
+ "sha256:4847d1f94affa3071a8b091857e46d0b0ecf646899f29bb50c5b8cf5eb276a9a",
+ "sha256:56f39e872e80e0eefc5c84f62588e2ec570decf892b2cbc2860d0bde01324e80",
+ "sha256:8f4930da4c5fea2ed43452647b9a7da693d0be475a0fd0da1433b324b2d1b1b6",
+ "sha256:91a9394690ba0fc6ca49dc14bc76a8334c7b5c95d6e1a06f09673a089d5a9eae",
+ "sha256:9a4b207690b1e5fd308540d92888203c9f193a8900ca0f9bb1536a0230fdabf4",
+ "sha256:9a9da74df7a3b238778af7922921a0063b85f97e172d853b806fb6d2c5354bec",
+ "sha256:a437b92b95d617bb16972697f756ebf1409ccce0070fa3db90b596c9d6f0a2b2",
+ "sha256:a678f2db5e31b1af88b2d70b7577b8e3400e4bc153ff8cc0b025cc966475220c",
+ "sha256:b0182debddf44a3b7b5ae2919cd0c719c61bc7eb8bb0dd9131052ed9f1305b5c",
+ "sha256:becc6d9c784f86c9411ea343a297df23e56d1d174b1b504f78f834663436eae5",
+ "sha256:c409de7030215c5d5d8cbb405164bbfb8e546732babbeb096f25a8975106d964",
+ "sha256:ce094f45e4fa1cf8f3980c445d7cd75706bd73002ef62fb666851d4683460372",
+ "sha256:e15cdfc73962f54d4a1a696774bd622ba0a8936d70dec2444bd85c71a02faab8",
+ "sha256:e6279dc78aeaae8341d57719d166dda8493f381091f0ea39829514562a98d3bb",
+ "sha256:e6312b9a3277fcf63576ed5c9b194d388911192d3f0138880471742c7d850efa",
+ "sha256:efb07dd5ab924f6c43147700fc1f3d0968ab229ff26952ca9d062539c7ba57c5",
+ "sha256:f5776a9a4798c6ef7d2d0ea66c15e06127c3d333ee4561db9bebf1262bf2dcd8"
],
"index": "pypi",
- "version": "==2.0.8"
+ "version": "==2.0.11"
},
"atomicwrites": {
"hashes": [
- "sha256:0312ad34fcad8fac3704d441f7b317e50af620823353ec657a53e981f92920c0",
- "sha256:ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee"
+ "sha256:03472c30eb2c5d1ba9227e4c2ca66ab8287fbfbbda3888aa93dc2e28fc6811b4",
+ "sha256:75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6"
],
- "markers": "python_version != '3.1.*' and python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.3.*' and python_version != '3.0.*'",
- "version": "==1.2.1"
+ "version": "==1.3.0"
},
"attrs": {
"hashes": [
@@ -97,27 +110,27 @@
},
"cryptography": {
"hashes": [
- "sha256:02602e1672b62e803e08617ec286041cc453e8d43f093a5f4162095506bc0beb",
- "sha256:10b48e848e1edb93c1d3b797c83c72b4c387ab0eb4330aaa26da8049a6cbede0",
- "sha256:17db09db9d7c5de130023657be42689d1a5f60502a14f6f745f6f65a6b8195c0",
- "sha256:227da3a896df1106b1a69b1e319dce218fa04395e8cc78be7e31ca94c21254bc",
- "sha256:2cbaa03ac677db6c821dac3f4cdfd1461a32d0615847eedbb0df54bb7802e1f7",
- "sha256:31db8febfc768e4b4bd826750a70c79c99ea423f4697d1dab764eb9f9f849519",
- "sha256:4a510d268e55e2e067715d728e4ca6cd26a8e9f1f3d174faf88e6f2cb6b6c395",
- "sha256:6a88d9004310a198c474d8a822ee96a6dd6c01efe66facdf17cb692512ae5bc0",
- "sha256:76936ec70a9b72eb8c58314c38c55a0336a2b36de0c7ee8fb874a4547cadbd39",
- "sha256:7e3b4aecc4040928efa8a7cdaf074e868af32c58ffc9bb77e7bf2c1a16783286",
- "sha256:8168bcb08403ef144ff1fb880d416f49e2728101d02aaadfe9645883222c0aa5",
- "sha256:8229ceb79a1792823d87779959184a1bf95768e9248c93ae9f97c7a2f60376a1",
- "sha256:8a19e9f2fe69f6a44a5c156968d9fc8df56d09798d0c6a34ccc373bb186cee86",
- "sha256:8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6",
- "sha256:be495b8ec5a939a7605274b6e59fbc35e76f5ad814ae010eb679529671c9e119",
- "sha256:dc2d3f3b1548f4d11786616cf0f4415e25b0fbecb8a1d2cd8c07568f13fdde38",
- "sha256:e4aecdd9d5a3d06c337894c9a6e2961898d3f64fe54ca920a72234a3de0f9cb3",
- "sha256:e79ab4485b99eacb2166f3212218dd858258f374855e1568f728462b0e6ee0d9",
- "sha256:f995d3667301e1754c57b04e0bae6f0fa9d710697a9f8d6712e8cca02550910f"
- ],
- "version": "==2.3.1"
+ "sha256:05b3ded5e88747d28ee3ef493f2b92cbb947c1e45cf98cfef22e6d38bb67d4af",
+ "sha256:06826e7f72d1770e186e9c90e76b4f84d90cdb917b47ff88d8dc59a7b10e2b1e",
+ "sha256:08b753df3672b7066e74376f42ce8fc4683e4fd1358d34c80f502e939ee944d2",
+ "sha256:2cd29bd1911782baaee890544c653bb03ec7d95ebeb144d714b0f5c33deb55c7",
+ "sha256:31e5637e9036d966824edaa91bf0aa39dc6f525a1c599f39fd5c50340264e079",
+ "sha256:42fad67d7072216a49e34f923d8cbda9edacbf6633b19a79655e88a1b4857063",
+ "sha256:4946b67235b9d2ea7d31307be9d5ad5959d6c4a8f98f900157b47abddf698401",
+ "sha256:522fdb2809603ee97a4d0ef2f8d617bc791eb483313ba307cb9c0a773e5e5695",
+ "sha256:6f841c7272645dd7c65b07b7108adfa8af0aaea57f27b7f59e01d41f75444c85",
+ "sha256:7d335e35306af5b9bc0560ca39f740dfc8def72749645e193dd35be11fb323b3",
+ "sha256:8504661ffe324837f5c4607347eeee4cf0fcad689163c6e9c8d3b18cf1f4a4ad",
+ "sha256:9260b201ce584d7825d900c88700aa0bd6b40d4ebac7b213857bd2babee9dbca",
+ "sha256:9a30384cc402eac099210ab9b8801b2ae21e591831253883decdb4513b77a3cd",
+ "sha256:9e29af877c29338f0cab5f049ccc8bd3ead289a557f144376c4fbc7d1b98914f",
+ "sha256:ab50da871bc109b2d9389259aac269dd1b7c7413ee02d06fe4e486ed26882159",
+ "sha256:b13c80b877e73bcb6f012813c6f4a9334fcf4b0e96681c5a15dac578f2eedfa0",
+ "sha256:bfe66b577a7118e05b04141f0f1ed0959552d45672aa7ecb3d91e319d846001e",
+ "sha256:e091bd424567efa4b9d94287a952597c05d22155a13716bf5f9f746b9dc906d3",
+ "sha256:fa2b38c8519c5a3aa6e2b4e1cf1a549b54acda6adb25397ff542068e73d1ed00"
+ ],
+ "version": "==2.5"
},
"cycler": {
"hashes": [
@@ -150,60 +163,58 @@
},
"future": {
"hashes": [
- "sha256:e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb"
+ "sha256:67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8"
],
"index": "pypi",
- "version": "==0.16.0"
+ "version": "==0.17.1"
},
- "gwpy": {
+ "gwosc": {
"hashes": [
- "sha256:3b6d2ba9a8844f6321c62ff3b9439f119e6447194b3d234944b5120a0856b5cc",
- "sha256:74c5066e19e2b10dd0571ac0f0bd588b302d1f6de639a994021a580bb90d93f4"
+ "sha256:18ed53e2b0260bc2f41bfebcc196465081d97b92860b7083e321f9c39fb98ee2",
+ "sha256:f1ba1c0f076ddcc323427e22ff4516ff0ca7bead72a0131c6314ec8afeb750e4"
],
- "index": "pypi",
- "version": "==0.12.2"
+ "version": "==0.3.4"
},
- "h5py": {
+ "gwpy": {
"hashes": [
- "sha256:0f8cd2acbacf3177b4427ed42639c911667b1f24d923388ab1f8ad466a12be5e",
- "sha256:11277e3879098f921ee9e29105b20591e1dfdd44963357399f2abaa1a280c560",
- "sha256:1241dec0c94ac32f3285cac1d6f44beabf80423e422ab03bd2686d731a8a9294",
- "sha256:17b8187de0b3a945d8e8d031e7eb6ece2fce90791f9c5fde36f4396bf38fdde1",
- "sha256:2f30007d0796788a454c1293262f19f25e6428317d3d386f78138fba2a44e37d",
- "sha256:308e0758587ee16d4e73e7f2f8aae8351091e343bf0a43d2f697f9535465c816",
- "sha256:37cacddf0e8209905f52537a8cf71da0dd9a4de62bd79247274c97b24a408997",
- "sha256:38a23bb599748adf23d77f74885c0de6f4a7d9baa42f74e476bbf90fba2b47dd",
- "sha256:47ab18b7b7bbc36fd2b606289b703b6f0ee915b923d6ad94dd17ac80ebffc280",
- "sha256:486c78330af0bf33f5077b51d1888c0739c3cd1a03d5aade0d48572b3b5690ca",
- "sha256:4e2183458d6ef1ae87dfb5d6acd0786359336cd9ac0ece6396c09b59fdaa3bd6",
- "sha256:51d0595c3e58814c831f6cd2b664a5bf9590e26262c1d541b380d041e4fcb3c0",
- "sha256:56d259d56822b70881760b243957f04a0cf133f0ec65eae6a33f562826aee899",
- "sha256:5e6e777653169a3cc24ea56bb3d8c845ea391f8914c35bb6f350b0753a52891c",
- "sha256:62bfb0ebb0f59e5dccc0b0dbbc0fc40dd1d1e09d04c0dc71f89790231531d4a2",
- "sha256:67d89b64debfa021b54aa6f24bbf008403bd144748a0148596b518bce80d2fc4",
- "sha256:6bf38571f555fa214493ec6349d29024cc5f313bf1715b09f236c553fd22ae4d",
- "sha256:9214ca445c18a37bfe9c165982c0e317e2f21f035c8d635d1c6d9fcbaf35b7a8",
- "sha256:ab0c52850428d2e86029935389379c2c97f752e76b616da851deec8a4484f8ec",
- "sha256:b2eff336697d8dfd712c5d93fef9f4e4d3e97d9d8c258801836b8664a239e07a",
- "sha256:bb33fabc0b8f3fe3bb0f8d6821b2fad5b2a64c27a0808e8d1c5c1e3362062064",
- "sha256:bd5353ab342bae1262b04745934cc1565df4cbc8d6a979a0c98f42209bd5c265",
- "sha256:bd73444efd1ac06dac27b8405bbe8791a02fd1bc8a2fa0e575257f90b7b57467",
- "sha256:bd932236a2ef91a75fee5d7f4ace80ab494c5a59cd092a67c9785ddb7fdc218c",
- "sha256:c45650de228ace7731e4280e14fb687f6d5c29cd666c5b22b42492b035e994d6",
- "sha256:d5c0c01da45f901a3d429e7ef9e7e22baa869e1affb8715f1bf94e6a30020740",
- "sha256:d75035db5bde802a29f4f29f18bb7548863d29ac90ccbf2c04c11799bbbba2c3",
- "sha256:dda88206dc9464923f27f601000bc5b152ac0bd6d0122f098d4f239150a70076",
- "sha256:e1c2ac5d0aa232c0f60fecc6bd1122346885086a176f939b91058c4c980cc226",
- "sha256:e626c65a8587921ebc7fb8d31a49addfdd0b9a9aa96315ea484c09803337b955"
+ "sha256:0b939629deb6eaea8d60cbe1faf242ddcc445e99392697e03fe7a37d80d798d6",
+ "sha256:3da53fb6da72cae31b172093be90bc528109aa471f6b94507d74dd6a087fb930"
],
- "version": "==2.8.0"
+ "index": "pypi",
+ "version": "==0.13.1"
},
- "idna": {
+ "h5py": {
"hashes": [
- "sha256:156a6814fb5ac1fc6850fb002e0852d56c0c8d2531923a51032d1b70760e186e",
- "sha256:684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16"
- ],
- "version": "==2.7"
+ "sha256:05750b91640273c69989c657eaac34b091abdd75efc8c4824c82aaf898a2da0a",
+ "sha256:082a27208aa3a2286e7272e998e7e225b2a7d4b7821bd840aebf96d50977abbb",
+ "sha256:08e2e8297195f9e813e894b6c63f79372582787795bba2014a2db6a2de95f713",
+ "sha256:0dd2adeb2e9de5081eb8dcec88874e7fd35dae9a21557be3a55a3c7d491842a4",
+ "sha256:0f94de7a10562b991967a66bbe6dda9808e18088676834c0a4dcec3fdd3bcc6f",
+ "sha256:106e42e2e01e486a3d32eeb9ba0e3a7f65c12fa8998d63625fa41fb8bdc44cdb",
+ "sha256:1606c66015f04719c41a9863c156fc0e6b992150de21c067444bcb82e7d75579",
+ "sha256:1854c4beff9961e477e133143c5e5e355dac0b3ebf19c52cf7cc1b1ef757703c",
+ "sha256:1e9fb6f1746500ea91a00193ce2361803c70c6b13f10aae9a33ad7b5bd28e800",
+ "sha256:2cca17e80ddb151894333377675db90cd0279fa454776e0a4f74308376afd050",
+ "sha256:30e365e8408759db3778c361f1e4e0fe8e98a875185ae46c795a85e9bafb9cdf",
+ "sha256:3206bac900e16eda81687d787086f4ffd4f3854980d798e191a9868a6510c3ae",
+ "sha256:3c23d72058647cee19b30452acc7895621e2de0a0bd5b8a1e34204b9ea9ed43c",
+ "sha256:407b5f911a83daa285bbf1ef78a9909ee5957f257d3524b8606be37e8643c5f0",
+ "sha256:4162953714a9212d373ac953c10e3329f1e830d3c7473f2a2e4f25dd6241eef0",
+ "sha256:5fc7aba72a51b2c80605eba1c50dbf84224dcd206279d30a75c154e5652e1fe4",
+ "sha256:713ac19307e11de4d9833af0c4bd6778bde0a3d967cafd2f0f347223711c1e31",
+ "sha256:71b946d80ef3c3f12db157d7778b1fe74a517ca85e94809358b15580983c2ce2",
+ "sha256:8cc4aed71e20d87e0a6f02094d718a95252f11f8ed143bc112d22167f08d4040",
+ "sha256:9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002",
+ "sha256:a744e13b000f234cd5a5b2a1f95816b819027c57f385da54ad2b7da1adace2f3",
+ "sha256:b087ee01396c4b34e9dc41e3a6a0442158206d383c19c7d0396d52067b17c1cb",
+ "sha256:b0f03af381d33306ce67d18275b61acb4ca111ced645381387a02c8a5ee1b796",
+ "sha256:b9e4b8dfd587365bdd719ae178fa1b6c1231f81280b1375eef8626dfd8761bf3",
+ "sha256:c5dd4ec75985b99166c045909e10f0534704d102848b1d9f0992720e908928e7",
+ "sha256:d2b82f23cd862a9d05108fe99967e9edfa95c136f532a71cb3d28dc252771f50",
+ "sha256:e58a25764472af07b7e1c4b10b0179c8ea726446c7141076286e41891bf3a563",
+ "sha256:f3b49107fbfc77333fc2b1ef4d5de2abcd57e7ea3a1482455229494cf2da56ce"
+ ],
+ "version": "==2.9.0"
},
"joblib": {
"hashes": [
@@ -243,48 +254,43 @@
"sha256:efabbcd4f406b532206b8801058c8bab9e79645b9880329253ae3322b7b02cd5",
"sha256:f923406e6b32c86309261b8195e24e18b6a8801df0cfc7814ac44017bfcb3939"
],
- "markers": "python_version != '3.2.*' and python_version != '3.0.*' and python_version != '3.1.*' and python_version >= '2.7' and python_version != '3.3.*'",
"version": "==1.0.1"
},
"lalsuite": {
"hashes": [
- "sha256:04851946d35129b4aaf8f70cdfeb8b907111cfa2910031b63c17f568e4309e13",
- "sha256:288c623c855f9806bcaac27aa66ad684c60317b11df756dc6b5c321a769e177f",
- "sha256:35450268f7e223ee9cf3246dfadfed80fd255d8312600329dc05d4bf582930bd",
- "sha256:3e074fb2caf2189def95eaa89f85d6f497ee957476c18e8adb5be05aab501f0a",
- "sha256:497f2ad84c5565e4e94e3696a5c4317ec4218b4070ee4a603c83e23147b81979",
- "sha256:61952d7301c2c62aade8e1382964d67628eb721fb42191de1fc89fcd995e8553",
- "sha256:a2d52070d946c76c1f5b3b4b37777136607b7285bf5aa485d978353666eaafdd",
- "sha256:dd91c8445e94d92c4add4ccb2806c12a8fde9493ea29ac78063bba8863ea7801",
- "sha256:df31cd918a20c82065f308184b39d9055f8271055d2da251c82aee85eceed244",
- "sha256:e5da42137d118ac3fb368a4353dad40c5bbdf4f6a1c1918b811d103658cd862d"
+ "sha256:0701de9dcc8687fcd6be9247e6d7d65a1126330b14d18b6b9fd01ac05af49b79",
+ "sha256:0f9807882957eb9c4987c054b1cc2d0c7f63f74a9cd591fa0832e15c7fccc88c",
+ "sha256:49dcae78ed93d3e01712d5222b12a9d4d68653340eb90c671669e29ea6f2e8a2",
+ "sha256:660f84245d94d7464112a4c88d1e5e97e100e2f499a57d939ccb08273a9904bd",
+ "sha256:81f402434c622824efba13e814bc7c3e668c434aa28b5c44a76ebd04c1886bc0",
+ "sha256:8741743f8825fca268d8496de54d27047304f2112c200a904d74e5f8a56aabc6",
+ "sha256:9029612981092048d7ac196b0718191c34a9d4dda9c907bd65ac5fbacf61f407",
+ "sha256:c421d8012046cada221c14f2834d704efd6342152ef6a45756efd2142d62b897",
+ "sha256:d24deb45e3e1fbf2b9590f0c2f3c0568e7756e65428ad7d2fa023f445717c2a2",
+ "sha256:fb3af5e25eddec819c3bf65d0d2ab5df1bfbf9235070980ea319a546ff78ed07"
],
"index": "pypi",
- "version": "==6.49"
+ "version": "==6.52"
},
"ligo-segments": {
"hashes": [
- "sha256:373edab42206aff8b5f2ef4417a40a0b0150c53ba6613424ce0d996ca56e9d1f",
- "sha256:6ac5bca4fe70325854f852ec2a6a30a36eddfa092fb370bd1865fee6ecc0d6e2",
- "sha256:7694c568d31cb37223ccedab55e304adb2d34a6f3832ae18316e0d636d249335",
- "sha256:871bca5de488f95b739837a8ebf84be91ba5116dfa20ce8f32e2f05b38b741d7",
- "sha256:94159ab427422d4434dc9c07516a89fd7360ad27a64cb3d81b2015a27cd551ed",
- "sha256:da4e2848b09046a1f81c03afd9c7293702c94a22b98d755e7d5806e65f206014"
+ "sha256:5edbcb88cae007c4e154a61cb2c9d0a6d6d4016c1ecaf0a59a667a267bd20e7a"
],
- "version": "==1.0.1"
+ "version": "==1.2.0"
},
"ligotimegps": {
"hashes": [
"sha256:48a8bd249e1822ddb484e4e59477654c333d1fe7d6b0de37249b2dcae72c5c99",
"sha256:79ee18df7f6806d522f68d278b0ac426094626a479af58c178f32d2b319919ba"
],
+ "index": "pypi",
"version": "==1.2.3"
},
"lscsoft-glue": {
"hashes": [
- "sha256:a0ddf26fbb45a19b046510e630b6d39a1798f4cd89ba883a38b4f2f491d39d2b"
+ "sha256:c51a5703e33c8ca244ab50723dd5bf3984c3c6383838e77e9dd451678024a2a6"
],
- "version": "==1.59.3"
+ "version": "==1.60.0"
},
"matplotlib": {
"hashes": [
@@ -324,11 +330,11 @@
},
"more-itertools": {
"hashes": [
- "sha256:c187a73da93e7a8acc0001572aebc7e3c69daf7bf6881a2cea10650bd4420092",
- "sha256:c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e",
- "sha256:fcbfeaea0be121980e15bc97b3817b5202ca73d0eae185b4550cbfce2a3ebb3d"
+ "sha256:38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4",
+ "sha256:c0a5785b1109a6bd7fac76d6837fd1feca158e54e521ccd2ae8bfe393cc9d4fc",
+ "sha256:fe7a7cae1ccb57d33952113ff4fa1bc5f879963600ed74918f1236e212ee50b9"
],
- "version": "==4.3.0"
+ "version": "==5.0.0"
},
"nestle": {
"hashes": [
@@ -339,35 +345,36 @@
},
"numexpr": {
"hashes": [
- "sha256:0a14dff7e893dd21f299993a6107437c2c7dd37a8aeb51933a8c0ff33ed1e036",
- "sha256:11f215d739495f3c88c9cdd84f0b7ee27b5c1d4348df9b16854933d8165a1f7b",
- "sha256:1374c5a996d1e48c64b26fad48fe2540c41f10436fbbe35cca61f35c57bcaeab",
- "sha256:21a9ea646a76b8fe98ac1e1fcd914c03addd3e4aa7feb040bc462b274a47b2cf",
- "sha256:21c05fb3ee1be0ff3be0d6ef572bf0e5dad27bf5d90c067e1580127340e36e2d",
- "sha256:2a05c3c6342b0c1416cb3e8eecaee5ce9387917781afc1a5d5c5f93f546b3735",
- "sha256:34e4381246893ac27c21c39356ef27ab7176d326f5a86b05486718f1f505f794",
- "sha256:3d1f2123d385e3790fc9f650950a79aaaa9ac62f8455bd9451263d29f37924f2",
- "sha256:4ddec358f5082ea941bb316a6aa1fec068dea6f7ed1f60a1089b03340c1f58af",
- "sha256:53f50dbbd1d41c7ae33bf6811f0a4a6a333ae592baf218e257c9e32190235cba",
- "sha256:58349f46670aa4d1cef14f9c794dda307bf8578d383c7e602fe36de112f6afa0",
- "sha256:5fc41e3652c7154ee5767a99b3fd72d81c3b01df364c42ccd2e89926c8fbbda5",
- "sha256:618e4058e6a707007aebbf74c37d8156ac0c26870dd6b8495678ba3fd9aaef79",
- "sha256:7419c43f1b22d3cd282480d753242588b2a0f449c6429f0999a2eebe0e5d7426",
- "sha256:7bde656a67ce5368cf1d748c569d0132baf9813c45860b872f3a35294067c1e4",
- "sha256:90cc7b1e051a57386d9b3125506a1a2f320964e017a9a5ce78a055b99e826ceb",
- "sha256:9415b24d6f79528ef85be3afe7871e0f49ae2bbe28cc9cb0272db4edd136e443",
- "sha256:9e292c060172f415888fb36f50fd2d4688797f66ec11eb9fbc33666cacbd5f68",
- "sha256:ae5dae4d34fc57c47167a7c79603f9592da504fc077833afc259451bc29cec4c",
- "sha256:bf62d6fa0453cec848c91179857a46e84f0812881d9bdfa29cda0672e599c9a5",
- "sha256:d304f4bfe69ca3e81a992a90c2a0e53c7fbc82769eedff32db8204496e223bbc",
- "sha256:e5456df5fabcd02f08aa06f0f61eee682649bd5e033ac7319f91a9f9c1d4d1c3",
- "sha256:e83bd5e6e424cf0a6e7d9de97d4ecd2d978eed478104f4c65496b8ea7d148268",
- "sha256:ed2c841e3ced875c34abc89987f5203fce53e563341e4f4b2ac615b419412f37",
- "sha256:edc4af30bbe504946d036ad9f2c849ff2c8a837d8df2c7f9f0b7d8497e982743",
- "sha256:ee8bc7201aa2f1962c67d27c326a11eef9df887d7b87b1278a1d4e722bf44375"
- ],
- "markers": "python_version != '3.2.*' and python_version != '3.0.*' and python_version != '3.1.*' and python_version >= '2.7' and python_version != '3.3.*'",
- "version": "==2.6.8"
+ "sha256:066d7202d3374d42203ce8ba2b007f14397fd083946abafebbc962215ead1759",
+ "sha256:08196ac987324dc02147abcf1883b192aa5cd1a56a07c725310f1d0d703d5301",
+ "sha256:37b04292cbb1e20bfb3428d5aeebe2bdd13368d458e508998087e40b68d8cc95",
+ "sha256:426053be016a3584a10cae13f18692938ff7314988f69edd367b4ff60b370b5b",
+ "sha256:47c205a2bca8477eaaa766ca2b86001ca0df4b61ae407196a3ba2420932b5dca",
+ "sha256:4b65fe1b4565ccaab7a3617da1bd046987fb7dbc0bbe34e56aa08b05857259d1",
+ "sha256:5839cd5f95b4088659cc5f6d25936c6a03a75c23be37f94a2885db0f6f234531",
+ "sha256:5fe05f123e00170370c759734c395e5a4ae0ad4e6a3d370fd73e0dcd6669e665",
+ "sha256:62d2853df0233fc04374679de20f39b93fdb7a664a0ee403fdb8e722328c5d4d",
+ "sha256:688a25cfcd7be6fcce3f6d59fffca6105541e7a1598144b545b633a266e94113",
+ "sha256:6a0470a6c07eaa6aa27affb9ee89ce91070747e44172870b020fd3ebe318950a",
+ "sha256:6b70a0c372bb567ddb3039d046cccede284cee2a43688010a4110f6b2fe59421",
+ "sha256:7f4e121bd59f3b5f7bbd9ca8873c815277c4994b22cfff8a7d57bdef9d00e939",
+ "sha256:8213a3e84f3afadc0a4ab1fc0dab383482297f36dbf84b690bbe698b9b8c2ece",
+ "sha256:97920e6c37553571ce55f951080d9e2b28589c1337c3788b5ae66dae3a0131d2",
+ "sha256:9992ef8b9598a62364d46d4cb2f0f6285f4c77115f023dca821a50550044d8fc",
+ "sha256:9c6b4dfcc978ad50a72f83fbaf0fe4706088f3b2623e365bc05036db4948e15d",
+ "sha256:9ef58b5f8debcf0c573968f44709866210696aa476b0d22d9afe88da2bd70add",
+ "sha256:a64bfd49359df8f87c34ed601ce857213d8678e314d8c99b972b36e35ff8f98f",
+ "sha256:aa5b238af8f2915b39374d764ec0daa3d0a975a798f162c3ca30f1cd9fa9a274",
+ "sha256:ae5c73f7412b7e70c88f6b384ad61e123d909b0c81a8d5edd33239eb9b5b3111",
+ "sha256:c3850466765b9b374ff2ff40974a7b4b278b875f94314e038043f534aff8e139",
+ "sha256:e99213c7fa5ffd5572afe065bab7a8507d750221e3fbba43fc15151056d108a1",
+ "sha256:eac513cd2424c5f1b2c75bcb06402da407d74bb6f72584d599218228060c2468",
+ "sha256:ecb0d0a1ac843f2b8c7afdc0c3ec4fcfcc275bbd0750065cc4112fcd14904c90",
+ "sha256:ed96bc38a37fc34406ef76595235e5966d7d3a4123018e9a91d1b7307b4af425",
+ "sha256:ee4c526517d89f92c9b9f9c1937ab15c9e3d33864213b4488e1dd30fbc43c87f",
+ "sha256:fc218b777cdbb14fa8cff8f28175ee631bacabbdd41ca34e061325b6c44a6fa6"
+ ],
+ "version": "==2.6.9"
},
"numpy": {
"hashes": [
@@ -405,59 +412,44 @@
},
"pandas": {
"hashes": [
- "sha256:11975fad9edbdb55f1a560d96f91830e83e29bed6ad5ebf506abda09818eaf60",
- "sha256:12e13d127ca1b585dd6f6840d3fe3fa6e46c36a6afe2dbc5cb0b57032c902e31",
- "sha256:1c87fcb201e1e06f66e23a61a5fea9eeebfe7204a66d99df24600e3f05168051",
- "sha256:242e9900de758e137304ad4b5663c2eff0d798c2c3b891250bd0bd97144579da",
- "sha256:26c903d0ae1542890cb9abadb4adcb18f356b14c2df46e4ff657ae640e3ac9e7",
- "sha256:2e1e88f9d3e5f107b65b59cd29f141995597b035d17cc5537e58142038942e1a",
- "sha256:31b7a48b344c14691a8e92765d4023f88902ba3e96e2e4d0364d3453cdfd50db",
- "sha256:4fd07a932b4352f8a8973761ab4e84f965bf81cc750fb38e04f01088ab901cb8",
- "sha256:5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4",
- "sha256:647b3b916cc8f6aeba240c8171be3ab799c3c1b2ea179a3be0bd2712c4237553",
- "sha256:66b060946046ca27c0e03e9bec9bba3e0b918bafff84c425ca2cc2e157ce121e",
- "sha256:6efa9fa6e1434141df8872d0fa4226fc301b17aacf37429193f9d70b426ea28f",
- "sha256:be4715c9d8367e51dbe6bc6d05e205b1ae234f0dc5465931014aa1c4af44c1ba",
- "sha256:bea90da782d8e945fccfc958585210d23de374fa9294a9481ed2abcef637ebfc",
- "sha256:d318d77ab96f66a59e792a481e2701fba879e1a453aefeebdb17444fe204d1ed",
- "sha256:d785fc08d6f4207437e900ffead930a61e634c5e4f980ba6d3dc03c9581748c7",
- "sha256:de9559287c4fe8da56e8c3878d2374abc19d1ba2b807bfa7553e912a8e5ba87c",
- "sha256:f4f98b190bb918ac0bc0e3dd2ab74ff3573da9f43106f6dba6385406912ec00f",
- "sha256:f71f1a7e2d03758f6e957896ed696254e2bc83110ddbc6942018f1a232dd9dad",
- "sha256:fb944c8f0b0ab5c1f7846c686bc4cdf8cde7224655c12edcd59d5212cd57bec0"
+ "sha256:295cf212054b28f1d111f3ffff932a012601558424ec892f2450d6197f6eeb92",
+ "sha256:29960ea1783c59fe86b323799b130592149e0f7bb739149e7fc512b0272d9fc3",
+ "sha256:29dde0874d1efb8a346f8d919b0530a9ae788ad1003752376133e38df09e6fcb",
+ "sha256:2d6b7b152a6ba44627c60df291f773c4438df01653abcbec7fc556d6039f1705",
+ "sha256:5de7275fc7222211dcac603ea81f1e143c45f8ec41d2e21df71aad0c95c1097c",
+ "sha256:7261b3567804a70714cc2591e2f7f1e372379db9e140f9d7ffb4b8884eaa48f7",
+ "sha256:758b8f6c68bc99b2eb64e57092d3aa07bd68a774e92e7686e473e0d9c86a2309",
+ "sha256:835c5a2aeaa3cb5ef2a1d771c75ee3a73d6ad1b82cfc54677c8f863c75fa51bd",
+ "sha256:8398d7a47ae667a639ac4ee6724d7ef98602b5ff2b10b5b4d5e6ab45a8d596d2",
+ "sha256:84ab1d50590cb2d9554211f164dc1b1a216bc94da2ba922aed2690c83f248fd9",
+ "sha256:98054c04318ba46bb81433230c2e5fab6a68df916ccb5355d428907bfb16b257",
+ "sha256:9e5ee41d1550ec36093c95e30644e313df4b57c1cdead545754d9c113aecbbb5",
+ "sha256:d4495aba61060d87c634fc777ac15aecd1d176987e5ed0585a3ed7e2f4e6c1f7",
+ "sha256:d5f72c8239e46cfcc363c7e532a474b7ea3d8892b7b6e5ec0da6b3ebae2a07d3",
+ "sha256:d88f484a25ac212fd720b5f9b9686e83f86df2b091b51f4b7b1d9089bd842f79"
],
"index": "pypi",
- "version": "==0.23.4"
- },
- "pathlib2": {
- "hashes": [
- "sha256:8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83",
- "sha256:d1aa2a11ba7b8f7b21ab852b1fb5afb277e1bb99d5dfc663380b5015c0d80c5a"
- ],
- "markers": "python_version < '3.6'",
- "version": "==2.3.2"
+ "version": "==0.23.0"
},
"patsy": {
"hashes": [
- "sha256:14269536ecedaae0a5a2f300faac7d0afa1cc47aa98c561f54ba7300d0ec4011",
- "sha256:e05f38d5c38c8d216f0cc2b765b1069b433c92d628b954fb2fee68d13e42883b"
+ "sha256:5465be1c0e670c3a965355ec09e9a502bf2c4cbe4875e8528b0221190a8a5d40",
+ "sha256:f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991"
],
- "markers": "python_version != '3.1.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.2.*' and python_version != '3.0.*'",
- "version": "==0.5.0"
+ "version": "==0.5.1"
},
"pbr": {
"hashes": [
- "sha256:1b8be50d938c9bb75d0eaf7eda111eec1bf6dc88a62a6412e33bf077457e0f45",
- "sha256:b486975c0cafb6beeb50ca0e17ba047647f229087bd74e37f4a7e2cac17d2caa"
+ "sha256:a7953f66e1f82e4b061f43096a4bcc058f7d3d41de9b94ac871770e8bdd831a2",
+ "sha256:d717573351cfe09f49df61906cd272abaa759b3e91744396b804965ff7bff38b"
],
- "version": "==4.2.0"
+ "version": "==5.1.2"
},
"pluggy": {
"hashes": [
"sha256:6e3836e39f4d36ae72840833db137f7b7d35105079aee6ec4a62d9f80d594dd1",
"sha256:95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1"
],
- "markers": "python_version != '3.1.*' and python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.3.*' and python_version != '3.0.*'",
"version": "==0.7.1"
},
"ptemcee": {
@@ -469,112 +461,99 @@
},
"py": {
"hashes": [
- "sha256:06a30435d058473046be836d3fc4f27167fd84c45b99704f2fb5509ef61f9af1",
- "sha256:50402e9d1c9005d759426988a492e0edaadb7f4e68bcddfea586bc7432d009c6"
+ "sha256:bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694",
+ "sha256:e76826342cefe3c3d5f7e8ee4316b80d1dd8a300781612ddbc765c17ba25a6c6"
],
- "markers": "python_version != '3.1.*' and python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.3.*' and python_version != '3.0.*'",
- "version": "==1.6.0"
+ "version": "==1.7.0"
},
"pycparser": {
"hashes": [
"sha256:a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3"
],
- "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.3.*' and python_version != '3.1.*' and python_version != '3.0.*'",
"version": "==2.19"
},
"pymc3": {
"hashes": [
- "sha256:49639eb62e14f7735ecbb03fa79f1c5f59f2e971c8ce0168b86ed1929e2c14ee",
- "sha256:6088e683c6d730bb21350a0f54ee083fa5a28e4d5ef52d57878141c9c20f21ee"
- ],
- "index": "pypi",
- "version": "==3.5"
- },
- "pymultinest": {
- "hashes": [
- "sha256:42f1f5efa13c99b9faebd205151ac6136adfb86bb428a714deb3f489daa58f06",
- "sha256:e5e76de90d226150659bc817e4a207556060bd91db1471e731d7734a7aa1826e"
+ "sha256:c00c0778d2451a348a9508f8b956fe280a0f9affd3f85140ac3948bc2902f5e9"
],
"index": "pypi",
- "version": "==2.6"
+ "version": "==3.6"
},
"pyopenssl": {
"hashes": [
- "sha256:26ff56a6b5ecaf3a2a59f132681e2a80afcc76b4f902f612f518f92c2a1bf854",
- "sha256:6488f1423b00f73b7ad5167885312bb0ce410d3312eb212393795b53c8caa580"
+ "sha256:aeca66338f6de19d1aa46ed634c3b9ae519a64b458f8468aec688e7e3c20f200",
+ "sha256:c727930ad54b10fc157015014b666f2d8b41f70c0d03e83ab67624fd3dd5d1e6"
],
- "version": "==18.0.0"
+ "version": "==19.0.0"
},
"pyparsing": {
"hashes": [
- "sha256:bc6c7146b91af3f567cf6daeaec360bc07d45ffec4cf5353f4d7a208ce7ca30a",
- "sha256:d29593d8ebe7b57d6967b62494f8c72b03ac0262b1eed63826c6f788b3606401"
+ "sha256:66c9268862641abcac4a96ba74506e594c884e3f57690a696d21ad8210ed667a",
+ "sha256:f6c5ef0d7480ad048c054c37632c67fca55299990fff127850181659eea33fc3"
],
- "markers": "python_version != '3.2.*' and python_version >= '2.6' and python_version != '3.1.*' and python_version != '3.0.*'",
- "version": "==2.2.2"
+ "version": "==2.3.1"
},
"pytest": {
"hashes": [
- "sha256:0a72d8a9f559c006ba153e0c9b4838efd7b656cf1f993747ba7128770d6eb12c",
- "sha256:95529588ff4e85114a0b0ad8e9cf0131ca47d46b28230e25366c5aba66b1d854"
+ "sha256:341ec10361b64a24accaec3c7ba5f7d5ee1ca4cebea30f76fad3dd12db9f0541",
+ "sha256:952c0389db115437f966c4c2079ae9d54714b9455190e56acebe14e8c38a7efa"
],
- "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.3.*' and python_version != '3.1.*' and python_version != '3.0.*'",
- "version": "==3.8.1"
+ "version": "==3.6.4"
},
"python-dateutil": {
"hashes": [
- "sha256:1adb80e7a782c12e52ef9a8182bebeb73f1d7e24e374397af06fb4956c8dc5c0",
- "sha256:e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8"
+ "sha256:7e6584c74aeed623791615e26efd690f29817a27c73085b78e4bad02493df2fb",
+ "sha256:c89805f6f4d64db21ed966fda138f8a5ed7a4fdbc1a8ee329ce1b74e3c74da9e"
],
- "version": "==2.7.3"
+ "version": "==2.8.0"
},
"pytz": {
"hashes": [
- "sha256:a061aa0a9e06881eb8b3b2b43f05b9439d6583c206d0a6c340ff72a7b6669053",
- "sha256:ffb9ef1de172603304d9d2819af6f5ece76f2e85ec10692a524dd876e72bf277"
+ "sha256:32b0891edff07e28efe91284ed9c31e123d84bea3fd98e1f72be2508f43ef8d9",
+ "sha256:d5f05e487007e29e03409f9398d074e158d920d36eb82eaf66fb1136b0c5374c"
],
- "version": "==2018.5"
+ "version": "==2018.9"
},
"scipy": {
"hashes": [
- "sha256:0611ee97296265af4a21164a5323f8c1b4e8e15c582d3dfa7610825900136bb7",
- "sha256:08237eda23fd8e4e54838258b124f1cd141379a5f281b0a234ca99b38918c07a",
- "sha256:0e645dbfc03f279e1946cf07c9c754c2a1859cb4a41c5f70b25f6b3a586b6dbd",
- "sha256:0e9bb7efe5f051ea7212555b290e784b82f21ffd0f655405ac4f87e288b730b3",
- "sha256:108c16640849e5827e7d51023efb3bd79244098c3f21e4897a1007720cb7ce37",
- "sha256:340ef70f5b0f4e2b4b43c8c8061165911bc6b2ad16f8de85d9774545e2c47463",
- "sha256:3ad73dfc6f82e494195144bd3a129c7241e761179b7cb5c07b9a0ede99c686f3",
- "sha256:3b243c77a822cd034dad53058d7c2abf80062aa6f4a32e9799c95d6391558631",
- "sha256:404a00314e85eca9d46b80929571b938e97a143b4f2ddc2b2b3c91a4c4ead9c5",
- "sha256:423b3ff76957d29d1cce1bc0d62ebaf9a3fdfaf62344e3fdec14619bb7b5ad3a",
- "sha256:42d9149a2fff7affdd352d157fa5717033767857c11bd55aa4a519a44343dfef",
- "sha256:625f25a6b7d795e8830cb70439453c9f163e6870e710ec99eba5722775b318f3",
- "sha256:698c6409da58686f2df3d6f815491fd5b4c2de6817a45379517c92366eea208f",
- "sha256:729f8f8363d32cebcb946de278324ab43d28096f36593be6281ca1ee86ce6559",
- "sha256:8190770146a4c8ed5d330d5b5ad1c76251c63349d25c96b3094875b930c44692",
- "sha256:878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1",
- "sha256:8b984f0821577d889f3c7ca8445564175fb4ac7c7f9659b7c60bef95b2b70e76",
- "sha256:8f841bbc21d3dad2111a94c490fb0a591b8612ffea86b8e5571746ae76a3deac",
- "sha256:c22b27371b3866c92796e5d7907e914f0e58a36d3222c5d436ddd3f0e354227a",
- "sha256:d0cdd5658b49a722783b8b4f61a6f1f9c75042d0e29a30ccb6cacc9b25f6d9e2",
- "sha256:d40dc7f494b06dcee0d303e51a00451b2da6119acbeaccf8369f2d29e28917ac",
- "sha256:d8491d4784aceb1f100ddb8e31239c54e4afab8d607928a9f7ef2469ec35ae01",
- "sha256:dfc5080c38dde3f43d8fbb9c0539a7839683475226cf83e4b24363b227dfe552",
- "sha256:e24e22c8d98d3c704bb3410bce9b69e122a8de487ad3dbfe9985d154e5c03a40",
- "sha256:e7a01e53163818d56eabddcafdc2090e9daba178aad05516b20c6591c4811020",
- "sha256:ee677635393414930541a096fc8e61634304bb0153e4e02b75685b11eba14cae",
- "sha256:f0521af1b722265d824d6ad055acfe9bd3341765735c44b5a4d0069e189a0f40",
- "sha256:f25c281f12c0da726c6ed00535ca5d1622ec755c30a3f8eafef26cf43fede694"
+ "sha256:02cb79ea38114dc480e9b08d6b87095728e8fb39b9a49b449ee443d678001611",
+ "sha256:03c827cdbc584e935264040b958e5fa0570a16095bee23a013482ba3f0e963a2",
+ "sha256:04f2b23258139c109d0524f111597dd095a505d9cb2c71e381d688d653877fa3",
+ "sha256:3132a9fab3f3545c8b0ba15688d11857efdd4a58d388d3785dc474f56fea7138",
+ "sha256:4b1f0883cb9d8ee963cf0a31c87341e9e758abb2cf1e5bcc0d7b066ef6b17573",
+ "sha256:4cce25c6e7ff7399c67dfe1b5423c36c391cf9b4b2be390c1675ab410f1ef503",
+ "sha256:51a2424c8ed80e60bdb9a896806e7adaf24a58253b326fbad10f80a6d06f2214",
+ "sha256:5706b785ca289fdfd91aa05066619e51d140613b613e35932601f2315f5d8470",
+ "sha256:58f0435f052cb60f1472c77f52a8f6642f8877b70559e5e0b9a1744f33f5cbe5",
+ "sha256:63e1d5ca9e5e1984f1a275276991b036e25d39d37dd7edbb3f4f6165c2da7dbb",
+ "sha256:64b2c35824da3ef6bb1e722216e4ef28802af6413c7586136500e343d34ba179",
+ "sha256:6f791987899532305126309578727c0197bddbafab9596bafe3e7bfab6e1ce13",
+ "sha256:72bd766f753fd32f072d30d7bc2ad492d56dbcbf3e13764e27635d5c41079339",
+ "sha256:7413080b381766a22d52814edb65631f0e323a7cea945c70021a672f38acc73f",
+ "sha256:78a67ee4845440e81cfbfabde20537ca12051d0eeac951fe4c6d8751feac3103",
+ "sha256:7994c044bf659b0a24ad7673ec7db85c2fadb87e4980a379a9fd5b086fe3649a",
+ "sha256:7dc4002f0a0a688774ef04878afe769ecd1ac21fe9b4b1d7125e2cf16170afd3",
+ "sha256:854bd87cc23824d5db4983956bc30f3790e1c7448f1a9e6a8fb7bff7601aef87",
+ "sha256:8608316d0cc01f8b25111c8adfe6efbc959cbba037a62c784551568d7ffbf280",
+ "sha256:8f5fcc87b48fc3dd6d901669c89af4feeb856dffb6f671539a238b7e8af1799c",
+ "sha256:937147086e8b4338bf139ca8fa98da650e3a46bf2ca617f8e9dd68c3971ec420",
+ "sha256:bc294841f6c822714af362095b181a853f47ed5ce757354bd2e4776d579ff3a4",
+ "sha256:bc6a88b0009a1b60eab5c22ac3a006f6968d6328de10c6a64ebb0d64a05548d3",
+ "sha256:c5eae911cf26b3c7eda889ec98d3c226f312c587acfaaf02602473f98b4c16d6",
+ "sha256:cca33a01a5987c650b87a1a910aa311ffa44e67cca1ff502ef9efdae5d9a8624",
+ "sha256:d1ae77b79fd5e27a10ba7c4e7c3a62927b9d29a4dccf28f6905c25d983aaf183",
+ "sha256:fb36064047e6bf87b6320a9b6eb7f525ef6863c7a4aef1a84a4bbfb043612617",
+ "sha256:fc1a19d95649439dbd50baca676bceb29bbfcd600aed2c5bd71d9bad82a87cfe"
],
"index": "pypi",
- "version": "==1.1.0"
+ "version": "==1.2.0"
},
"six": {
"hashes": [
- "sha256:70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9",
- "sha256:832dc0e10feb1aa2c68dcc57dbb658f1c7e65b9b61af69048abc87a2db00a0eb"
+ "sha256:3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c",
+ "sha256:d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73"
],
- "version": "==1.11.0"
+ "version": "==1.12.0"
},
"tables": {
"hashes": [
@@ -592,29 +571,30 @@
"sha256:bdc5c073712af2a43babd139c4855fc99496bb2c3f3f5d1b4770a985e6f9ce29",
"sha256:bed4f423dd33600907f1c3b88f994920f2b879b12bf83d4372f861ef4085e085",
"sha256:c3ac22e3391f67a381d9a3018fd7e0a1ccfcc88b5f61b0d051fe5eba8196388f",
+ "sha256:d263f4380a5dad862efac774428bacb04c2339c4f165f2efdd228867abaffcf6",
"sha256:da98c8abfeefefad40110b994d5d06ac28d89b00d085530d377376b201566ebf",
"sha256:e2e4e40d010a6aa0464e5e281d4aa15f64acd99fd881c0e1e4c1c567b7167dba",
"sha256:e3bd7084dbf80ef347ad5d33645584e0fe7f8353cf2c33d8922a4c00034fa015",
"sha256:e8f9b20b9623c900e7007b89a9d3e315280b666ac70b38b0c191345f7d4d8585",
"sha256:f786d310cf954eaf52340680dfbc5c1190afc276093f5c454fab605a11488306",
- "sha256:f97c8b5ebec23894fc56af25c6e73bc86b463cbccb1f9b9887def24cd7811e2c"
+ "sha256:f97c8b5ebec23894fc56af25c6e73bc86b463cbccb1f9b9887def24cd7811e2c",
+ "sha256:fd3e774ff048de838df39b018c171bff3ecd9f34a908395a475ba07ac270a34a"
],
"version": "==3.4.4"
},
"theano": {
"hashes": [
- "sha256:637f3b34d40ef5e0d54dd4c40618475aaa085c26d2491e925c98e2ad4bc2115a"
+ "sha256:35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913"
],
"index": "pypi",
- "version": "==1.0.3"
+ "version": "==1.0.4"
},
"tqdm": {
"hashes": [
- "sha256:18f1818ce951aeb9ea162ae1098b43f583f7d057b34d706f66939353d1208889",
- "sha256:df02c0650160986bac0218bb07952245fc6960d23654648b5d5526ad5a4128c9"
+ "sha256:13f018038711256ed27aae118a80d63929588e90f00d072a0f4eb7aa3333b4dc",
+ "sha256:dd60ea2567baa013c625153ce41fd274209c69a5814513e1d635f20e5cd61b97"
],
- "markers": "python_version != '3.1.*' and python_version >= '2.6' and python_version != '3.0.*'",
- "version": "==4.26.0"
+ "version": "==4.30.0"
}
},
"develop": {}
diff --git a/bilby/core/result.py b/bilby/core/result.py
index 691812db9dadcac7b8f6792f9aa6191090869e8d..5c95f1e834fc7eb0b43f2c28d7a5b38335d1d725 100644
--- a/bilby/core/result.py
+++ b/bilby/core/result.py
@@ -157,7 +157,15 @@ class Result(object):
else:
filename = result_file_name(outdir, label)
if os.path.isfile(filename):
- return cls(**deepdish.io.load(filename))
+ dictionary = deepdish.io.load(filename)
+ # Some versions of deepdish/pytables return the dictionanary as
+ # a dictionary with a kay 'data'
+ if len(dictionary) == 1 and 'data' in dictionary:
+ dictionary = dictionary['data']
+ try:
+ return cls(**dictionary)
+ except TypeError as e:
+ raise IOError("Unable to load dictionary, error={}".format(e))
else:
raise IOError("No result '{}' found".format(filename))
diff --git a/bilby/core/sampler/__init__.py b/bilby/core/sampler/__init__.py
index 76b1589b2f5f0af474779fa776dcd495557f58a2..7a15b410cb1fb9ef4d425610a16bbd3c9d4ccc3b 100644
--- a/bilby/core/sampler/__init__.py
+++ b/bilby/core/sampler/__init__.py
@@ -11,20 +11,21 @@ from .cpnest import Cpnest
from .dynesty import Dynesty
from .emcee import Emcee
from .nestle import Nestle
+from .polychord import PyPolyChord
from .ptemcee import Ptemcee
from .ptmcmc import PTMCMCSampler
from .pymc3 import Pymc3
from .pymultinest import Pymultinest
-implemented_samplers = {
+IMPLEMENTED_SAMPLERS = {
'cpnest': Cpnest, 'dynesty': Dynesty, 'emcee': Emcee, 'nestle': Nestle,
'ptemcee': Ptemcee,'ptmcmcsampler' : PTMCMCSampler,
- 'pymc3': Pymc3, 'pymultinest': Pymultinest }
+ 'pymc3': Pymc3, 'pymultinest': Pymultinest, 'pypolychord': PyPolyChord }
if command_line_args.sampler_help:
sampler = command_line_args.sampler_help
- if sampler in implemented_samplers:
- sampler_class = implemented_samplers[sampler]
+ if sampler in IMPLEMENTED_SAMPLERS:
+ sampler_class = IMPLEMENTED_SAMPLERS[sampler]
print('Help for sampler "{}":'.format(sampler))
print(sampler_class.__doc__)
else:
@@ -33,7 +34,7 @@ if command_line_args.sampler_help:
'the name of the sampler')
else:
print('Requested sampler {} not implemented'.format(sampler))
- print('Available samplers = {}'.format(implemented_samplers))
+ print('Available samplers = {}'.format(IMPLEMENTED_SAMPLERS))
sys.exit()
@@ -106,7 +107,7 @@ def run_sampler(likelihood, priors=None, label='label', outdir='outdir',
if command_line_args.clean:
kwargs['resume'] = False
- from . import implemented_samplers
+ from . import IMPLEMENTED_SAMPLERS
if priors is None:
priors = dict()
@@ -128,15 +129,15 @@ def run_sampler(likelihood, priors=None, label='label', outdir='outdir',
if isinstance(sampler, Sampler):
pass
elif isinstance(sampler, str):
- if sampler.lower() in implemented_samplers:
- sampler_class = implemented_samplers[sampler.lower()]
+ if sampler.lower() in IMPLEMENTED_SAMPLERS:
+ sampler_class = IMPLEMENTED_SAMPLERS[sampler.lower()]
sampler = sampler_class(
likelihood, priors=priors, outdir=outdir, label=label,
injection_parameters=injection_parameters, meta_data=meta_data,
use_ratio=use_ratio, plot=plot, result_class=result_class,
**kwargs)
else:
- print(implemented_samplers)
+ print(IMPLEMENTED_SAMPLERS)
raise ValueError(
"Sampler {} not yet implemented".format(sampler))
elif inspect.isclass(sampler):
@@ -148,7 +149,7 @@ def run_sampler(likelihood, priors=None, label='label', outdir='outdir',
else:
raise ValueError(
"Provided sampler should be a Sampler object or name of a known "
- "sampler: {}.".format(', '.join(implemented_samplers.keys())))
+ "sampler: {}.".format(', '.join(IMPLEMENTED_SAMPLERS.keys())))
if sampler.cached_result:
logger.warning("Using cached result")
diff --git a/bilby/core/sampler/polychord.py b/bilby/core/sampler/polychord.py
new file mode 100644
index 0000000000000000000000000000000000000000..4378649335da69a5a4e852e9831b19b40c5d0c9a
--- /dev/null
+++ b/bilby/core/sampler/polychord.py
@@ -0,0 +1,94 @@
+from __future__ import absolute_import
+
+import numpy as np
+
+from .base_sampler import NestedSampler
+
+
+class PyPolyChord(NestedSampler):
+
+ """
+ Bilby wrapper of PyPolyChord
+ https://arxiv.org/abs/1506.00171
+
+ PolyChordLite is available at:
+ https://github.com/PolyChord/PolyChordLite
+
+ Follow the installation instructions at their github page.
+
+ Keyword arguments will be passed into `pypolychord.run_polychord` into the `settings`
+ argument. See the PolyChord documentation for what all of those mean.
+
+ To see what the keyword arguments are for, see the docstring of PyPolyChordSettings
+ """
+
+ default_kwargs = dict(use_polychord_defaults=False, nlive=None, num_repeats=None,
+ nprior=-1, do_clustering=True, feedback=1, precision_criterion=0.001,
+ logzero=-1e30, max_ndead=-1, boost_posterior=0.0, posteriors=True,
+ equals=True, cluster_posteriors=True, write_resume=True,
+ write_paramnames=False, read_resume=True, write_stats=True,
+ write_live=True, write_dead=True, write_prior=True,
+ compression_factor=np.exp(-1), base_dir='outdir',
+ file_root='polychord', seed=-1, grade_dims=None, grade_frac=None, nlives={})
+
+ def run_sampler(self):
+ import pypolychord
+ from pypolychord.settings import PolyChordSettings
+ if self.kwargs['use_polychord_defaults']:
+ settings = PolyChordSettings(nDims=self.ndim, nDerived=self.ndim, base_dir=self.outdir,
+ file_root=self.label)
+ else:
+ self._setup_dynamic_defaults()
+ pc_kwargs = self.kwargs.copy()
+ pc_kwargs['base_dir'] = self.outdir
+ pc_kwargs['file_root'] = self.label
+ pc_kwargs.pop('use_polychord_defaults')
+ settings = PolyChordSettings(nDims=self.ndim, nDerived=self.ndim, **pc_kwargs)
+ self._verify_kwargs_against_default_kwargs()
+
+ pypolychord.run_polychord(loglikelihood=self.log_likelihood, nDims=self.ndim,
+ nDerived=self.ndim, settings=settings, prior=self.prior_transform)
+
+ self.result.log_evidence, self.result.log_evidence_err = self._read_out_stats_file()
+ self.result.samples = self._read_sample_file()
+ return self.result
+
+ def _setup_dynamic_defaults(self):
+ """ Sets up some interdependent default argument if none are given by the user """
+ if not self.kwargs['grade_dims']:
+ self.kwargs['grade_dims'] = [self.ndim]
+ if not self.kwargs['grade_frac']:
+ self.kwargs['grade_frac'] = [1.0] * len(self.kwargs['grade_dims'])
+ if not self.kwargs['nlive']:
+ self.kwargs['nlive'] = self.ndim * 25
+ if not self.kwargs['num_repeats']:
+ self.kwargs['num_repeats'] = self.ndim * 5
+
+ def _translate_kwargs(self, kwargs):
+ if 'nlive' not in kwargs:
+ for equiv in self.npoints_equiv_kwargs:
+ if equiv in kwargs:
+ kwargs['nlive'] = kwargs.pop(equiv)
+
+ def log_likelihood(self, theta):
+ """ Overrides the log_likelihood so that PolyChord understands it """
+ return super(PyPolyChord, self).log_likelihood(theta), theta
+
+ def _read_out_stats_file(self):
+ statsfile = self.outdir + '/' + self.label + '.stats'
+ with open(statsfile) as f:
+ for line in f:
+ if line.startswith('log(Z)'):
+ line = line.replace('log(Z)', '')
+ line = line.replace('=', '')
+ line = line.replace(' ', '')
+ print(line)
+ z = line.split('+/-')
+ log_z = float(z[0])
+ log_z_err = float(z[1])
+ return log_z, log_z_err
+
+ def _read_sample_file(self):
+ sample_file = self.outdir + '/' + self.label + '_equal_weights.txt'
+ samples = np.loadtxt(sample_file)
+ return samples[:, -self.ndim:] # extract last ndim columns
diff --git a/docs/samplers.txt b/docs/samplers.txt
index ee37613391531e9917b0ff9af8256b27efc12203..c497beb6ab8806cb9fb790fd316de59d0c0b7570 100644
--- a/docs/samplers.txt
+++ b/docs/samplers.txt
@@ -48,7 +48,7 @@ you would use
is given in the API information below.
Below, we give the detailed API for the samplers. Remember, this API is not
-recomended for direct use by the user, rather it should be accessed via the
+recommended for direct use by the user, rather it should be accessed via the
:code:`run_sampler`.
---------------
@@ -60,6 +60,7 @@ Dynesty
.. autoclass:: bilby.core.sampler.dynesty.Dynesty
+
Nestle
======
@@ -71,11 +72,19 @@ CPNest
.. autoclass:: bilby.core.sampler.cpnest.Cpnest
+
PyMultinest
===========
.. autoclass:: bilby.core.sampler.pymultinest.Pymultinest
+
+PyPolyChord
+===========
+
+.. autoclass:: bilby.core.sampler.pypolychord.PyPolyChord
+
+
-------------
MCMC samplers
-------------
@@ -123,6 +132,27 @@ be found in the at the top-level of `the repository
<https://git.ligo.org/lscsoft/bilby>`_ (Note: if you installed from pip, you
can simply download that file and use the command above).
+
+Installing PyPolyChord
+======================
+
+If you want to use the `PyPolyChord` sampler, you first need the
+PolyChord library to be installed to work properly. An image of PolyChord can be found on github.
+Clone the following repository onto your system. Navigate to the folder you want to install PolyChord in and run:
+
+.. code-block:: console
+
+ $ git clone https://github.com/PolyChord/PolyChordLite.git
+
+Then navigate into the PolyChord directory and install PolyChord/PyPolyChord with
+
+.. code-block:: console
+
+ $ make pypolychord MPI=
+ $ python setup.py install --user
+
+Add a number after `MPI=` to compile with `MPI`. Leave it like it is if you don't wish to compile with MPI.
+
Installing pymultinest
======================
diff --git a/test/sampler_test.py b/test/sampler_test.py
index 0ffbb2bac84f0096fa8dc7e20052b0ad1ee09b78..3054ad4ae52d57b88ae31e0dc217069d2c0c0f5b 100644
--- a/test/sampler_test.py
+++ b/test/sampler_test.py
@@ -5,6 +5,8 @@ import unittest
from mock import MagicMock
import numpy as np
import os
+import sys
+import shutil
import copy
@@ -247,6 +249,53 @@ class TestNestle(unittest.TestCase):
self.assertDictEqual(expected, self.sampler.kwargs)
+class TestPolyChord(unittest.TestCase):
+
+ def setUp(self):
+ self.likelihood = MagicMock()
+ self.priors = dict(a=bilby.prior.Uniform(0, 1))
+ self.sampler = bilby.core.sampler.PyPolyChord(self.likelihood, self.priors,
+ outdir='outdir', label='polychord',
+ use_ratio=False, plot=False,
+ skip_import_verification=True)
+
+ def tearDown(self):
+ del self.likelihood
+ del self.priors
+ del self.sampler
+
+ def test_default_kwargs(self):
+ expected = dict(use_polychord_defaults=False, nlive=self.sampler.ndim*25, num_repeats=self.sampler.ndim*5,
+ nprior=-1, do_clustering=True, feedback=1, precision_criterion=0.001,
+ logzero=-1e30, max_ndead=-1, boost_posterior=0.0, posteriors=True,
+ equals=True, cluster_posteriors=True, write_resume=True,
+ write_paramnames=False, read_resume=True, write_stats=True,
+ write_live=True, write_dead=True, write_prior=True,
+ compression_factor=np.exp(-1), base_dir='outdir',
+ file_root='polychord', seed=-1, grade_dims=list([self.sampler.ndim]),
+ grade_frac=list([1.0]*len([self.sampler.ndim])), nlives={})
+ self.sampler._setup_dynamic_defaults()
+ self.assertDictEqual(expected, self.sampler.kwargs)
+
+ def test_translate_kwargs(self):
+ expected = dict(use_polychord_defaults=False, nlive=123, num_repeats=self.sampler.ndim*5,
+ nprior=-1, do_clustering=True, feedback=1, precision_criterion=0.001,
+ logzero=-1e30, max_ndead=-1, boost_posterior=0.0, posteriors=True,
+ equals=True, cluster_posteriors=True, write_resume=True,
+ write_paramnames=False, read_resume=True, write_stats=True,
+ write_live=True, write_dead=True, write_prior=True,
+ compression_factor=np.exp(-1), base_dir='outdir',
+ file_root='polychord', seed=-1, grade_dims=list([self.sampler.ndim]),
+ grade_frac=list([1.0]*len([self.sampler.ndim])), nlives={})
+ self.sampler._setup_dynamic_defaults()
+ for equiv in bilby.core.sampler.base_sampler.NestedSampler.npoints_equiv_kwargs:
+ new_kwargs = self.sampler.kwargs.copy()
+ del new_kwargs['nlive']
+ new_kwargs[equiv] = 123
+ self.sampler.kwargs = new_kwargs
+ self.assertDictEqual(expected, self.sampler.kwargs)
+
+
class TestPTEmcee(unittest.TestCase):
def setUp(self):
@@ -397,11 +446,13 @@ class TestRunningSamplers(unittest.TestCase):
self.priors = dict(
m=bilby.core.prior.Uniform(0, 5), c=bilby.core.prior.Uniform(-2, 2))
+ bilby.core.utils.check_directory_exists_and_if_not_mkdir('outdir')
def tearDown(self):
del self.likelihood
del self.priors
bilby.core.utils.command_line_args.test = False
+ shutil.rmtree('outdir')
def test_run_cpnest(self):
_ = bilby.run_sampler(
@@ -423,6 +474,11 @@ class TestRunningSamplers(unittest.TestCase):
likelihood=self.likelihood, priors=self.priors, sampler='nestle',
nlive=100, save=False)
+ def test_run_pypolychord(self):
+ _ = bilby.run_sampler(
+ likelihood=self.likelihood, priors=self.priors,
+ sampler='pypolychord', nlive=100, save=False)
+
def test_run_ptemcee(self):
_ = bilby.run_sampler(
likelihood=self.likelihood, priors=self.priors, sampler='ptemcee',