diff --git a/Dockerfile b/Dockerfile
index 7dabf4b0b49f1aaa4e36f10128596fb699f1bd79..6bbdf3350c9b1ffd19ce22defae3a68c1324655b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -39,11 +39,12 @@ RUN useradd \
-r \
-s /sbin/nologin \
geomag_user \
- && mkdir -p /home/geomag_user/notebooks \
- && chown -R geomag_user:geomag_user /home/geomag_user
+ && mkdir -p /data \
+ && chown -R geomag_user:geomag_user /data
USER geomag_user
-WORKDIR /geomag-algorithms
+WORKDIR /data
EXPOSE 8000
+
# entrypoint needs double quotes
ENTRYPOINT [ "/geomag-algorithms/docker-entrypoint.sh" ]
diff --git a/Pipfile b/Pipfile
index f4a876a15befe2441831448f3a46580fc8ce0093..77f7a9714748a12cb07aadd0d276b1b1335bc83c 100644
--- a/Pipfile
+++ b/Pipfile
@@ -4,15 +4,16 @@ url = "https://pypi.org/simple"
verify_ssl = true
[dev-packages]
+black = "*"
+pre-commit = "*"
pytest = "*"
pytest-cov = "*"
webtest = "*"
-black = "*"
[packages]
numpy = "*"
scipy = "*"
-obspy = "*"
+obspy = ">1.2.0"
pycurl = "*"
authlib = "*"
flask = "*"
@@ -21,7 +22,6 @@ flask-migrate = "*"
flask-session = "*"
flask-sqlalchemy = "*"
psycopg2-binary = "*"
-pre-commit = "*"
[pipenv]
allow_prereleases = true
diff --git a/Pipfile.lock b/Pipfile.lock
index accad7644ba26575276c8fc39d1ff00f5823bc93..f545cb84c02ef2aef8ab82996347c2472570c6cd 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
{
"_meta": {
"hash": {
- "sha256": "4f9084e7eebba8286a08bc6b827445c19a66a1864b730e9cf290509ed2224253"
+ "sha256": "0d3a780c71738929a0e69a18e14cdd60dc314f1f400dcf5015ad125cd2e9172c"
},
"pipfile-spec": 6,
"requires": {},
@@ -20,13 +20,6 @@
],
"version": "==1.4.1"
},
- "appdirs": {
- "hashes": [
- "sha256:9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92",
- "sha256:d8b24664561d0d34ddfaec54636d502d7cea6e29c3eaf68f3df6180863e2166e"
- ],
- "version": "==1.4.3"
- },
"authlib": {
"hashes": [
"sha256:89d55b14362f8acee450f9d153645e438e3a38be99b599190718c4406f575b05",
@@ -75,13 +68,6 @@
],
"version": "==1.14.0"
},
- "cfgv": {
- "hashes": [
- "sha256:1ccf53320421aeeb915275a196e23b3b8ae87dea8ac6698b1638001d4a486d53",
- "sha256:c8e8f552ffcc6194f4e18dd4f68d9aef0c0d58ae7e7be8c82bee3c5e9edfa513"
- ],
- "version": "==3.1.0"
- },
"chardet": {
"hashes": [
"sha256:84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae",
@@ -91,10 +77,10 @@
},
"click": {
"hashes": [
- "sha256:2335065e6395b9e67ca716de5f7526736bfa6ceead690adf616d925bdc622b13",
- "sha256:5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7"
+ "sha256:8a18b4ea89d8820c5d0c7da8a64b2c324b4dabb695804dbfea19b9be9d88c0cc",
+ "sha256:e345d143d80bf5ee7534056164e5e112ea5e22716bbb1ce727941f4c8b471b9a"
],
- "version": "==7.0"
+ "version": "==7.1.1"
},
"cryptography": {
"hashes": [
@@ -136,19 +122,6 @@
],
"version": "==4.4.2"
},
- "distlib": {
- "hashes": [
- "sha256:2e166e231a26b36d6dfe35a48c4464346620f8645ed0ace01ee31822b288de21"
- ],
- "version": "==0.3.0"
- },
- "filelock": {
- "hashes": [
- "sha256:18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59",
- "sha256:929b7d63ec5b7d6b71b0fa5ac14e030b3f70b75747cef1b10da9b879fef15836"
- ],
- "version": "==3.0.12"
- },
"flask": {
"hashes": [
"sha256:13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52",
@@ -195,13 +168,6 @@
],
"version": "==0.18.2"
},
- "identify": {
- "hashes": [
- "sha256:1222b648251bdcb8deb240b294f450fbf704c7984e08baa92507e4ea10b436d5",
- "sha256:d824ebe21f38325c771c41b08a95a761db1982f1fc0eee37c6c97df3f1636b96"
- ],
- "version": "==1.4.11"
- },
"idna": {
"hashes": [
"sha256:7588d1c14ae4c77d74036e8c22ff447b26d0fde8f007354fd48a7814db15b7cb",
@@ -209,22 +175,6 @@
],
"version": "==2.9"
},
- "importlib-metadata": {
- "hashes": [
- "sha256:06f5b3a99029c7134207dd882428a66992a9de2bef7c2b699b5641f9886c3302",
- "sha256:b97607a1a18a5100839aec1dc26a1ea17ee0d93b20b0f008d80a5a050afb200b"
- ],
- "markers": "python_version < '3.8'",
- "version": "==1.5.0"
- },
- "importlib-resources": {
- "hashes": [
- "sha256:6aefffdf63634bd94600dd0691fd6430902272bace0572934fa23c81473a7ff7",
- "sha256:ce84b1c9c05078e1797700505bd1bc386cee9561002a9bdcfcba634adc6333e5"
- ],
- "markers": "python_version < '3.7'",
- "version": "==1.2.0"
- },
"itsdangerous": {
"hashes": [
"sha256:321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19",
@@ -360,28 +310,22 @@
},
"matplotlib": {
"hashes": [
- "sha256:019db591268b51dd30de5f3a8bbbf69589207e2d461de91c3aa425db6f135d3d",
- "sha256:14d8b073d5a23094b84e0fda7a4460215e98cc18917e8a71bb143fd18930660b",
- "sha256:23c186a5c521670f831bbd1f076ef1658e07a8cce3c7e8be1da0c828e86e08db",
- "sha256:2bbd55057ae22283bccca6251259dfeb6b5eaf0d7d2ce1cc963c2fb03174b50d",
- "sha256:42904319a69afcf36d27acfe9dc605cad2f19175d1e7e1a51a1e6f1c6515ba2a",
- "sha256:4a78312908e92f453ea554fb32290b51e4df799f4c31ec99f04c87dbb3553b18",
- "sha256:647a457c42ba4bd3a989384e1961a1f8766617a6519c4e53d6d3b215fad96756",
- "sha256:797cb1c5eed0f09bc7f16ae01b6cafc90e0768fd4809b7716e806ae693b10f89",
- "sha256:7b59131aaa13edcbe96a0d7d2d7d3a83a39749a39e97cc701f7355c2060f9945",
- "sha256:a396ea75cd64e0f730ef2a397dabcc894db702f496f2d9c3cb978daa6588220c",
- "sha256:a7d917bbe3f6de06c42d25df32003a527424ff367726e7a55e8daad53d6189d4",
- "sha256:b54cf89cb6400f1a8753a7b6479b6bf75fdfedff5fdb4ccc4458fadf245ae5ff",
- "sha256:c40a6d3455dcd37f3726e8e289b85f9df0125afb12cc3aeb781104c6390cae58",
- "sha256:d9be08267fc44f1eee2f13f603633726f6752780a72e0f0973c6ade5b35e98fe"
- ],
- "version": "==3.2.0rc3"
- },
- "nodeenv": {
- "hashes": [
- "sha256:5b2438f2e42af54ca968dd1b374d14a1194848955187b0e5e4be1f73813a5212"
- ],
- "version": "==1.3.5"
+ "sha256:0711b07920919951b2c508a773c433cbe07bdad952ea84ed9d18ca7853ccbe8b",
+ "sha256:0ab307e610302971012dc2387c97fc68e58c8eb00045a2c735da1b16353a3e3f",
+ "sha256:651d76daf9168250370d4befb09f79875daa2224a9096d97dfc3ed764c842be4",
+ "sha256:8e931015769322ee6860cabb8f975f628788e851092fd5edbdb065b5a516e3af",
+ "sha256:97a03e73f9ab71db8e4084894550c3af420c8ab1989b5e1306261b17576bf61b",
+ "sha256:9d174cc9681184023a7d520079eb0c085208761c6562710c1de7263d08217ab6",
+ "sha256:b21479a4478070c1c0f460e1bf1b65341e6a70ae0da905fcee836651450c66bb",
+ "sha256:b93377c6720e7db9cbba57e856a21aae2ff707677a6ee6b3b9d485f22ed82697",
+ "sha256:be937f34047bc09ed22d6a19d970fdc61d5d3191aa62f3262fc7f308e6d2e7f9",
+ "sha256:d281862a68b0bfce8f9e02a8e5acaa5cfbec37f37320f59b52eaf54b6423ec13",
+ "sha256:d5287cfcabad6f0f71a2627c1bbb6fb0cddacb9844f6c91f210604faa508f562",
+ "sha256:d75f5e952562f5e494ae92c1f917fc96c2ce09305a7c1bdc2e6502d3c61fbdc3",
+ "sha256:ee8acb1d4ee204e5cfe361d8f00d7e52c68f81c099b6c6048a3c76bf2c6b46e6",
+ "sha256:fc84f7c7cf1c5a9dbceadb7546818228f019d3b113ce5e362120c895fbba2944"
+ ],
+ "version": "==3.2.0"
},
"numpy": {
"hashes": [
@@ -412,26 +356,20 @@
},
"obspy": {
"hashes": [
- "sha256:14e7ff1b87c2cb901f3a6bebb64cbc5e8d624a067319c242b55cf77c341018fc",
- "sha256:17786240e76629b2e2004232fe97a988c9de5f91e2d3367906598760e0f86fa8",
- "sha256:20dbfdfffcbcea675f3749132eddf7ec4fb4e1defb23372573dcb8669651aa9d",
- "sha256:290dea98f7a8577911dae7816aae9117adc536b0baf6dde1db0b02c53b108a96",
- "sha256:5693b17ef7e7b62e69d28af0732d8f53beea35f64aba3c6a4e0b0996e1f5123e",
- "sha256:6141112cf264c7baf345333f6b32effefdc268098f499cc1bc7f14587af17149",
- "sha256:6268fceec0a8e717fb3eafd9cf25cc2ead9f956e3e7149ca10124ee488a9901c",
- "sha256:ce6fe921980bd877d91abda2b1046b95222b304ba2f50800a932979c87ec1c82",
- "sha256:d4f61569702a9cbc4bd00ea54589437ee220edd68c56168c6ebf6710e7e93bcd"
- ],
- "index": "pypi",
- "version": "==1.1.1"
- },
- "pre-commit": {
- "hashes": [
- "sha256:09ebe467f43ce24377f8c2f200fe3cd2570d328eb2ce0568c8e96ce19da45fa6",
- "sha256:f8d555e31e2051892c7f7b3ad9f620bd2c09271d87e9eedb2ad831737d6211eb"
+ "sha256:340905ecc6d6d29dfc7103808e74e23e1fcfcbbc6ac32d07accce9a8b0322f47",
+ "sha256:3476c417c9b57689cf387df379518c8115874179bc4b16424de0cde7ed014e18",
+ "sha256:876d42c15c8c857a0a51ddd1e9ba699711fb6efdd27201819721d25a42472e1c",
+ "sha256:8f58c53dc69f6f21b8d5ceefeec2ccf8ba8c738e28a6da2cb8b103890c6b3ff1",
+ "sha256:95c2dcf36fe33f6bbb592ccd8ef929565987ca663ceb052daa6a153751f2535a",
+ "sha256:b04152950827534e91a625afa09f9390caabce4f96adbe4571b39a832ca3e423",
+ "sha256:b4869de3d6de9d5c4f8fd6ad41d280fdbf99458ac9b8f5062bc2d9e92f132df7",
+ "sha256:baa15abec717cc2acfe3d8c87d9a68785c82513b8c69de0895a943c5da33095c",
+ "sha256:d94537b3b24b0023c09caeea4a2ca1e647f0a28264475c3fcbbfd9bc2df85dbd",
+ "sha256:f4b574e2c7278b6c8c96aaaf5f7ce4a497c54ef6b3358ad88397d4971b0973bf",
+ "sha256:ff507e10a21eee2a4e2930f5b3844e8b008b7d04f0f19f8d8a2e7de85a98ba86"
],
"index": "pypi",
- "version": "==2.1.1"
+ "version": "==1.2.1"
},
"psycopg2-binary": {
"hashes": [
@@ -473,9 +411,10 @@
},
"pycparser": {
"hashes": [
- "sha256:a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3"
+ "sha256:2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0",
+ "sha256:7582ad22678f0fcd81102833f60ef8d0e57288b6b5fb00323d101be910e35705"
],
- "version": "==2.19"
+ "version": "==2.20"
},
"pycurl": {
"hashes": [
@@ -514,22 +453,6 @@
],
"version": "==1.0.4"
},
- "pyyaml": {
- "hashes": [
- "sha256:059b2ee3194d718896c0ad077dd8c043e5e909d9180f387ce42012662a4946d6",
- "sha256:1cf708e2ac57f3aabc87405f04b86354f66799c8e62c28c5fc5f88b5521b2dbf",
- "sha256:24521fa2890642614558b492b473bee0ac1f8057a7263156b02e8b14c88ce6f5",
- "sha256:4fee71aa5bc6ed9d5f116327c04273e25ae31a3020386916905767ec4fc5317e",
- "sha256:70024e02197337533eef7b85b068212420f950319cc8c580261963aefc75f811",
- "sha256:74782fbd4d4f87ff04159e986886931456a1894c61229be9eaf4de6f6e44b99e",
- "sha256:940532b111b1952befd7db542c370887a8611660d2b9becff75d39355303d82d",
- "sha256:cb1f2f5e426dc9f07a7681419fe39cee823bb74f723f36f70399123f439e9b20",
- "sha256:dbbb2379c19ed6042e8f11f2a2c66d39cceb8aeace421bfc29d085d93eda3689",
- "sha256:e3a057b7a64f1222b56e47bcff5e4b94c4f61faac04c7c4ecb1985e18caa3994",
- "sha256:e9f45bd5b92c7974e59bcd2dcc8631a6b6cc380a904725fce7bc08872e691615"
- ],
- "version": "==5.3"
- },
"requests": {
"hashes": [
"sha256:43999036bfa82904b6af1d99e4882b560e5e2c68e5c4b0aa03b655f3d7d73fee",
@@ -573,16 +496,9 @@
},
"sqlalchemy": {
"hashes": [
- "sha256:64a7b71846db6423807e96820993fa12a03b89127d278290ca25c0b11ed7b4fb"
- ],
- "version": "==1.3.13"
- },
- "toml": {
- "hashes": [
- "sha256:229f81c57791a41d65e399fc06bf0848bab550a9dfd5ed66df18ce5f05e73d5c",
- "sha256:235682dd292d5899d361a811df37e04a8828a5b1da3115886b73cf81ebc9100e"
+ "sha256:b92d2de62e43499d85b1780274d1b562e5159c7996f6f04a9bb46cf681ced45f"
],
- "version": "==0.10.0"
+ "version": "==1.3.14"
},
"urllib3": {
"hashes": [
@@ -591,27 +507,12 @@
],
"version": "==1.25.8"
},
- "virtualenv": {
- "hashes": [
- "sha256:30ea90b21dabd11da5f509710ad3be2ae47d40ccbc717dfdd2efe4367c10f598",
- "sha256:4a36a96d785428278edd389d9c36d763c5755844beb7509279194647b1ef47f1"
- ],
- "version": "==20.0.7"
- },
"werkzeug": {
"hashes": [
"sha256:169ba8a33788476292d04186ab33b01d6add475033dfc07215e6d219cc077096",
"sha256:6dc65cf9091cf750012f56f2cad759fa9e879f511b5ff8685e456b4e3bf90d16"
],
"version": "==1.0.0"
- },
- "zipp": {
- "hashes": [
- "sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b",
- "sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"
- ],
- "markers": "python_version < '3.8'",
- "version": "==3.1.0"
}
},
"develop": {
@@ -645,12 +546,19 @@
"index": "pypi",
"version": "==19.10b0"
},
+ "cfgv": {
+ "hashes": [
+ "sha256:1ccf53320421aeeb915275a196e23b3b8ae87dea8ac6698b1638001d4a486d53",
+ "sha256:c8e8f552ffcc6194f4e18dd4f68d9aef0c0d58ae7e7be8c82bee3c5e9edfa513"
+ ],
+ "version": "==3.1.0"
+ },
"click": {
"hashes": [
- "sha256:2335065e6395b9e67ca716de5f7526736bfa6ceead690adf616d925bdc622b13",
- "sha256:5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7"
+ "sha256:8a18b4ea89d8820c5d0c7da8a64b2c324b4dabb695804dbfea19b9be9d88c0cc",
+ "sha256:e345d143d80bf5ee7534056164e5e112ea5e22716bbb1ce727941f4c8b471b9a"
],
- "version": "==7.0"
+ "version": "==7.1.1"
},
"coverage": {
"hashes": [
@@ -688,20 +596,25 @@
],
"version": "==5.0.3"
},
- "entrypoints": {
+ "distlib": {
"hashes": [
- "sha256:589f874b313739ad35be6e0cd7efde2a4e9b6fea91edcc34e58ecbb8dbe56d19",
- "sha256:c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451"
+ "sha256:2e166e231a26b36d6dfe35a48c4464346620f8645ed0ace01ee31822b288de21"
],
- "version": "==0.3"
+ "version": "==0.3.0"
},
- "flake8": {
+ "filelock": {
"hashes": [
- "sha256:45681a117ecc81e870cbf1262835ae4af5e7a8b08e40b944a8a6e6b895914cfb",
- "sha256:49356e766643ad15072a789a20915d3c91dc89fd313ccd71802303fd67e4deca"
+ "sha256:18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59",
+ "sha256:929b7d63ec5b7d6b71b0fa5ac14e030b3f70b75747cef1b10da9b879fef15836"
],
- "index": "pypi",
- "version": "==3.7.9"
+ "version": "==3.0.12"
+ },
+ "identify": {
+ "hashes": [
+ "sha256:1222b648251bdcb8deb240b294f450fbf704c7984e08baa92507e4ea10b436d5",
+ "sha256:d824ebe21f38325c771c41b08a95a761db1982f1fc0eee37c6c97df3f1636b96"
+ ],
+ "version": "==1.4.11"
},
"importlib-metadata": {
"hashes": [
@@ -711,12 +624,13 @@
"markers": "python_version < '3.8'",
"version": "==1.5.0"
},
- "mccabe": {
+ "importlib-resources": {
"hashes": [
- "sha256:ab8a6258860da4b6677da4bd2fe5dc2c659cff31b3ee4f7f5d64e79735b80d42",
- "sha256:dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f"
+ "sha256:1dff36d42d94bd523eeb847c25c7dd327cb56686d74a26dfcc8d67c504922d59",
+ "sha256:7f0e1b2b5f3981e39c52da0f99b2955353c5a139c314994d1126c2551ace9bdf"
],
- "version": "==0.6.1"
+ "markers": "python_version < '3.7'",
+ "version": "==1.3.1"
},
"more-itertools": {
"hashes": [
@@ -725,12 +639,18 @@
],
"version": "==8.2.0"
},
+ "nodeenv": {
+ "hashes": [
+ "sha256:5b2438f2e42af54ca968dd1b374d14a1194848955187b0e5e4be1f73813a5212"
+ ],
+ "version": "==1.3.5"
+ },
"packaging": {
"hashes": [
- "sha256:170748228214b70b672c581a3dd610ee51f733018650740e98c7df862a583f73",
- "sha256:e665345f9eef0c621aa0bf2f8d78cf6d21904eef16a93f020240b704a57f1334"
+ "sha256:3c292b474fda1671ec57d46d739d072bfd495a4f51ad01a055121d81e952b7a3",
+ "sha256:82f77b9bee21c1bafbf35a84905d604d5d1223801d639cf3ed140bd651c08752"
],
- "version": "==20.1"
+ "version": "==20.3"
},
"pathspec": {
"hashes": [
@@ -746,6 +666,14 @@
],
"version": "==0.13.1"
},
+ "pre-commit": {
+ "hashes": [
+ "sha256:09ebe467f43ce24377f8c2f200fe3cd2570d328eb2ce0568c8e96ce19da45fa6",
+ "sha256:f8d555e31e2051892c7f7b3ad9f620bd2c09271d87e9eedb2ad831737d6211eb"
+ ],
+ "index": "pypi",
+ "version": "==2.1.1"
+ },
"py": {
"hashes": [
"sha256:5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa",
@@ -753,20 +681,6 @@
],
"version": "==1.8.1"
},
- "pycodestyle": {
- "hashes": [
- "sha256:95a2219d12372f05704562a14ec30bc76b05a5b297b21a5dfe3f6fac3491ae56",
- "sha256:e40a936c9a450ad81df37f549d676d127b1b66000a6c500caa2b085bc0ca976c"
- ],
- "version": "==2.5.0"
- },
- "pyflakes": {
- "hashes": [
- "sha256:17dbeb2e3f4d772725c777fabc446d5634d1038f234e77343108ce445ea69ce0",
- "sha256:d976835886f8c5b31d47970ed689944a0262b5f3afa00a5a7b4dc81e5449f8a2"
- ],
- "version": "==2.1.1"
- },
"pyparsing": {
"hashes": [
"sha256:4c830582a84fb022400b85429791bc551f1f4871c33f23e44f353119e92f969f",
@@ -790,6 +704,22 @@
"index": "pypi",
"version": "==2.8.1"
},
+ "pyyaml": {
+ "hashes": [
+ "sha256:059b2ee3194d718896c0ad077dd8c043e5e909d9180f387ce42012662a4946d6",
+ "sha256:1cf708e2ac57f3aabc87405f04b86354f66799c8e62c28c5fc5f88b5521b2dbf",
+ "sha256:24521fa2890642614558b492b473bee0ac1f8057a7263156b02e8b14c88ce6f5",
+ "sha256:4fee71aa5bc6ed9d5f116327c04273e25ae31a3020386916905767ec4fc5317e",
+ "sha256:70024e02197337533eef7b85b068212420f950319cc8c580261963aefc75f811",
+ "sha256:74782fbd4d4f87ff04159e986886931456a1894c61229be9eaf4de6f6e44b99e",
+ "sha256:940532b111b1952befd7db542c370887a8611660d2b9becff75d39355303d82d",
+ "sha256:cb1f2f5e426dc9f07a7681419fe39cee823bb74f723f36f70399123f439e9b20",
+ "sha256:dbbb2379c19ed6042e8f11f2a2c66d39cceb8aeace421bfc29d085d93eda3689",
+ "sha256:e3a057b7a64f1222b56e47bcff5e4b94c4f61faac04c7c4ecb1985e18caa3994",
+ "sha256:e9f45bd5b92c7974e59bcd2dcc8631a6b6cc380a904725fce7bc08872e691615"
+ ],
+ "version": "==5.3"
+ },
"regex": {
"hashes": [
"sha256:01b2d70cbaed11f72e57c1cfbaca71b02e3b98f739ce33f5f26f71859ad90431",
@@ -863,6 +793,13 @@
],
"version": "==1.4.1"
},
+ "virtualenv": {
+ "hashes": [
+ "sha256:10750cac3b5a9e6eed54d0f1f8222c550dc47f84609c95cbc504d44a58a048b8",
+ "sha256:8512e83f1d90f8e481024d58512ac9c053bf16f54d9138520a0929396820dd78"
+ ],
+ "version": "==20.0.10"
+ },
"waitress": {
"hashes": [
"sha256:045b3efc3d97c93362173ab1dfc159b52cfa22b46c3334ffc805dbdbf0e4309e",
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
index 88e66799c41fe657cb05a106b60b99862377b346..14037016dc2bebea89fd041dd902c68bdfd7928b 100755
--- a/docker-entrypoint.sh
+++ b/docker-entrypoint.sh
@@ -1,24 +1,11 @@
#! /bin/bash
-# run jupyter in the background, and forward SIGTERM manually.
-# "exec" seems like a much simpler solution for this,
-# however, jupyter kernels die noisy deaths when using exec.
-
-# _term () {
-# echo 'Caught SIGTERM'
-# kill -TERM "$child"
-#}
-#trap _term SIGTERM
-
# add geomagio to notebook path
export PYTHONPATH=/geomag-algorithms
# run jupyter notebook server
exec jupyter notebook \
--ip='*' \
- --notebook-dir=/home/geomag_user/notebooks \
+ --notebook-dir=/data \
--no-browser \
--port=8000
-
-#child=$!
-#wait "$child"
diff --git a/docs/install.md b/docs/install.md
index 9c7b6dd04ff897ae1e141f18394291e4e355bf4f..2217fb7366b3926fb0dbf44c72d8c58ae440bd2f 100644
--- a/docs/install.md
+++ b/docs/install.md
@@ -1,26 +1,42 @@
-Installation
-============
+# Installation
+> - [Develop](./develop.md) describes how to install locally.
+> - [Docker](./install_docker.md) describes container usage.
+## Requirements:
-1) Install Python and dependencies (obspy and pycurl)
+- Python 3.6 or newer
+- ObsPy 1.2.1 or newer
- Using Anaconda is recommended ( https://conda.io/miniconda.html ).
+## Procedure:
- conda env create -f geomagenv.yml
- source activate geomagenv
+1. Install Python and dependencies
- or
+ - Option 1: Anaconda/Miniconda (https://conda.io/miniconda.html):
- conda create --name=geomagenv --channel conda-forge python=3 obspy pycurl
- source activate geomagenv
+ conda create --name=geomagenv --channel conda-forge python=3 obspy pycurl
+ source activate geomagenv
-2) Install **geomagio**
+ - Option 2: Pip
- pip install git+https://github.com/usgs/geomag-algorithms.git
+ > `pyenv` can install specific/multiple versions of python
+ >
+ > - https://github.com/pyenv/pyenv
+ > - https://github.com/pyenv-win/pyenv-win
+
+ # create virtual environment (optional)
+ python -m venv path/to/geomagenv
+ source path/to/geomagenv/bin/activate
+
+ # install dependencies
+ pip install numpy
+ pip install obspy
+2. Install **geomagio**
+
+ pip install git+https://github.com/usgs/geomag-algorithms.git
-3) Use **geomagio**
+3. Use **geomagio**
- Use the main script, `geomag.py -h`
- In python scripts, `import geomagio`
diff --git a/docs/install_docker.md b/docs/install_docker.md
index 1571d1f17b7697baaeaf17e91f0f25b227325404..02beede915bb904b4b3084e664176f4b9b1fd17a 100644
--- a/docs/install_docker.md
+++ b/docs/install_docker.md
@@ -1,60 +1,55 @@
## Docker
+
https://www.docker.com/
Docker containers bundle all dependencies needed to use geomag-algorithms.
The container includes a Jupyter Notebook server for interactive development.
-> Docker images are built using the `Dockerfile` at the root of this project.
+### Run docker container
+> This page provides one example of how to run a container. See https://docs.docker.com/engine/reference/run/ for detailed `docker run` documentation.
-### Create a new docker container
+The following command creates and starts a container in the background.
-The following command creates and starts a container.
-```
-docker run -d --name geomagio -p 8000:80 usgs/geomag-algorithms
-```
+ docker run --rm -it --name geomagio -p 8000:8000 -v $(pwd)/data:/data usgs/geomag-algorithms
-- `-d` runs container in the background
+- `--rm` runs a temporary container
+- `-it` makes the container interactive (so you can stop it with `ctrl+c`)
- `-name geomagio` assigns the name `geomagio`
-- `-p 8000:80` forwards system port `8000` to container port `80`
+- `-p 8000:8000` forwards system port `8000` to container port `8000`
+- `-v $(pwd)/data:/data` mounts a local data directory (./data) into the container so notebooks are saved
- `usgs/geomag-algorithms:latest` refers to the
latest version of the geomag-algorithms docker image
- > Notebooks are stored in the container in the directory
- > `/home/geomag_user/notebooks`
-
-
### Use the container
-- Start a stopped container:
-```
-docker start geomagio
-```
-
- Run an interactive python prompt
-```
-docker exec -it geomagio python
-```
+
+
+ docker exec -it geomagio python
- Use the Jupyter Notebook server
-```
-open http://localhost:8000/
-```
+
+ Check the output for a URL like this, that can be opened in a web browser: `http://127.0.0.1:8000/?token=...`
- Use the `geomag.py` command line interface
-```
-docker exec -it geomagio geomag.py \
- --inchannels H E Z F \
- --input edge \
- --interval minute \
- --observatory BOU \
- --output iaga2002 \
- --output-stdout \
- --starttime 2016-07-04T00:00:00Z \
- --endtime 2016-07-04T23:59:00Z
-```
+
+ docker exec -it geomagio geomag.py \
+ --inchannels H E Z F \
+ --input edge \
+ --interval minute \
+ --observatory BOU \
+ --output iaga2002 \
+ --output-stdout \
+ --starttime 2016-07-04T00:00:00Z \
+ --endtime 2016-07-04T23:59:00Z
- Stop a running container:
-```
-docker stop geomagio
-```
+
+ Press `Ctrl+C` and follow prompts to stop the container.
+
+### Build container
+
+Docker images are built using the `Dockerfile` at the root of this project.
+
+ docker build -t usgs/geomag-algorithms:TAG .
diff --git a/setup.py b/setup.py
index be3a710e5295b110d352dd3777f6e9ec3c2b34d9..6c243cf175d10649de6bf63153a207bf83b73bc3 100644
--- a/setup.py
+++ b/setup.py
@@ -1,28 +1,24 @@
+import os
import setuptools
+import setuptools.ssl_support
+
+# configure ssl certifiate bundle from environment, if set
+ssl_cert_file = os.environ.get("SSL_CERT_FILE") or os.environ.get("PIP_CERT")
+if ssl_cert_file:
+ setuptools.ssl_support.cert_paths = [ssl_cert_file]
setuptools.setup(
name="geomag-algorithms",
- version="1.0.1",
+ version="1.0.2",
description="USGS Geomag Algorithms Library",
url="https://github.com/usgs/geomag-algorithms",
packages=setuptools.find_packages(exclude=["test*"]),
- python_requires=">=3.6, <4",
- install_requires=["numpy", "scipy", "obspy"],
- extras_require={
- "url": ["pycurl"],
- "webservice": [
- "authlib",
- "flask",
- "flask-login",
- "flask-migrate",
- "flask-session",
- "flask-sqlalchemy",
- "psycopg2-binary",
- ],
- },
- scripts=["bin/geomag.py", "bin/geomag_webservice.py", "bin/make_cal.py"],
project_urls={
"Bug Reports": "https://github.com/usgs/geomag-algorithms/issues",
"Source": "https://github.com/usgs/geomag-algorithms",
},
+ python_requires=">=3.6, <4",
+ scripts=["bin/geomag.py", "bin/geomag_webservice.py", "bin/make_cal.py"],
+ setup_requires=["setuptools-pipfile",],
+ use_pipfile=True,
)